Now, having overcome a string of planning objections and other obstacles, the project is finally nearing completion and will open in spring 2007. All the evidence suggests that it will be a success, providing a stunning environment in which to view the extraordinary treasures from the Acropolis that are currently dispersed around other Athenian museums and elsewhere in the world.
Situated at the foot of the southern slopes of the Acropolis, the new £63m complex will provide a central unifying focus for the varied archaeology that is clustered around the site. It will also reunite numerous architectural and sculptural fragments currently displayed in the cramped and antiquated facilities of the existing Acropolis Museum, which was built between 1861 and 1874.
The new museum was co-funded by the Greek Ministry of Culture and the European Union and has been beset by controversy from the outset. Archaeological excavation of the site in the Makriyianni district directly beneath the Acropolis began in 1997, but in 2003 ran into objections from local residents which slowed down progress on the building.
It is a measure of the determination of the Organisation for the Construction of the New Acropolis Museum, in particular its president, the archaeologist Dimitrios Pandermalis, that opposition was finally overcome in July 2004. The excavations unearthed important ruins, including private houses of the early Christian era (400-600AD), and more than 50,000 portable antiquities - sculptures, lamps, vases, coins and domestic artefacts.
Those involved with the project believe that the detractors have finally been silenced. 'I don't believe there is any real controversy at the heart of this project,' insists Pandermalis. 'True, it raised many kinds of questions. "Is it the right place in which to build?", for example. But why should it be negative? If it had been a private project - a hotel, a block of flats - it would have been OK. So why not a museum?'
In a recent book, the museum's architect Bernard Tschumi wrote of the 'triple challenge' presented by the New Acropolis Museum - 'How to make an architectural statement at the foot of one of the most influential buildings of all time; how to design a building on a site already occupied by extensive archaeological excavations and in an earthquake-prone region; and how to design a museum to contain an important collection of classical Greek sculptures and a singular masterpiece, the Parthenon frieze, currently still housed
in the British Museum?'
Tschumi's solution appears to have succeeded on the first two counts at least. He has designed the 14,000 sq metre museum to maximise the ambient natural light of the region. Using seismic technology in its foundations, which absorbs 70 per cent of quake tremors, the building features an internal 'cella' exactly mirroring the orientation of the Parthenon, with the same number of columns (clad in stainless steel) as its ancient counterpart, accurate to the millimetre.
The base of the building floats on slender pillars above the 2,500 sq metre archaeological site and houses the lobby, temporary exhibition space, shops and other visitor facilities. This level has been fitted with a series of glazed floor panels revealing the excavated remains beneath. The middle section, a large trapezoidal plate, accommodates the Archaic collection, other permanent galleries and a mezzanine restaurant.
The top floor climaxes with the Parthenon Gallery, which contains the High Classical achievements of Periclean Athens. This floor also affords an entirely new vantage point from which to view the south side of the Acropolis and its associated monuments. The effect on reaching this upper level is a heart-stopping sense of space and light. While the lower level is orientated in relation to the archaeological remains, the upper floors conform to the orientation of the ancient monument. In Pandermalis's words: 'The lower floor fits to the site and the upper floor fits to the broader environment.'
The visitor is guided from level to level via a series of gentle ramps, echoing the approach to the Acropolis itself. Everywhere there are subtle reverberations of the architect Tschumi's interlinking of concept, context and content.
It is in the upper galleries that the surviving fragments of the Greek sculptor Pheidias's Parthenon frieze and metopes will be displayed next year - at any rate those still in Greek hands.
In stark contrast to the display in the British Museum's Duveen gallery, the sculptures will be arranged in the New Acropolis Museum for the first time in strict relation to their original arrangement on the Parthenon, itself visible through the impressive curtain windows enveloping the building. Pandermalis describes this as 'a visual dialogue, a cultural platform to the Parthenon and the Acropolis'.
Walking around the unfinished upper floors today, one is aware of a series of apertures in the cella, punctuated by blank walls and windows, that will ultimately be filled by sculptures - or left vacant, depending on the outcome of negotiations with the British Museum.
'The openings you see now represent sculptures held in Athens,' explains Pandermalis. 'The door cavities represent the destruction by the Venetian mercenary army under General Morosini in 1687. The vacant walls represent objects in London.'
And there's the rub. Whether the finished building will help persuade the British Museum, the Louvre and other 'encyclopaedic' museums around the world to surrender those pieces of the Parthenon in their collections - and so 'complete' the process of unification at the heart of the Acropolis project - remains to be seen. If it succeeds, the new museum could create a benchmark in cooperative cultural relations.
But if it fails, will the museum become notable for what it does not contain rather than for what it does?
Pandermalis is adamant that the museum is not a shrine to absence. Rather, the gaps are intended to be an eloquent appeal for unification, to strengthen the case for the return of the pieces held in London and elsewhere. 'The Parthenon Hall makes clear the continuity between the various components. The pieces we have of the frieze are of very high quality, so you can clearly imagine how they would have been on the original building. In a second, we can tell the story of the Parthenon Marbles as it has never been told before. I don't know of another museum in the world where you can get the feeling of the original unit of an ancient artistic complex all the time - the opposite of the idea of a fragmentary culture.'
Until the London pieces are returned, one of the main attractions of the Parthenon Gallery will be the West Frieze, recently cleaned using cutting-edge laser technology, but presently housed in the gloom of the old Acropolis Museum.
Christina Vlassopoulou, who supervised the conservation of the West Frieze, is excited that so many objects will finally be appreciated within the ambient natural light of the new building. They include the famous Kritios Boy, which will become one of the focal points of the new Archaic Gallery.
'He will be more articulate because he will be shown in context with other athletic figures such as bronzes found on the Acropolis that are now in the National Archaeological Museum,' says Vlassopoulou. 'You will also be able to see the back of a kore [statue of a woman], so we will have opportunities to do things we've not been able to do before.'
Vlassopoulou and her colleagues - who pioneered new techniques in conservation now being used elsewhere in the world - are still discovering fragments on the monument that relate to pieces in store or already on display. Conservation techniques have been developed to allow objects to be dismantled and reassembled to incorporate recent finds.
The new museum will provide an opportunity to monitor these processes, and to share them with the public. This corresponds with Pandermalis's vision of the new museum as an evolving work in progress. Hence no single grand opening has been planned. Instead, the museum will, he says, open 'throughout 2007'.
'There will be many steps in the opening process,' says Pandermalis. 'It is a museum of an archaeological site. The museum is about connecting pieces and it is interesting to show people the process by which we put things together. It will be a museum in action.'
Elena Korka, the director of prehistorical and classical antiquities of the archaeological service in Athens, lived on the Makriyianni site as a child and feels a deep emotional connection with the New Acropolis Museum. She believes it could widen the debate about the 'universal museum' that has become one of the most contested ideas in international museology in recent years.
'As a scholar and a member of the archaeological service, it is a dream come true,' says Korka. 'I think it's a universal museum in its own way. You don't need to have the old type of universal museum to have a universal museum; it's the message that comes out of the museum that counts. And if we follow what the British Museum has been talking about recently in terms of a new enlightenment, well that keeps coming from the Acropolis, from the Parthenon. It's a never-ending procedure. It's the way each society of every century grasps the message, uses it for the needs of its time, the needs of each society, so it's a universal contribution.'
The old Acropolis Museum currently attracts about 1.5 million people each year. The Greeks hope their new museum will at least double that figure. Clearly the return of the 'Elgin' Marbles would help them achieve that target.
But Neil MacGregor, the director of the British Museum, told the Financial Times a couple of years ago that: 'The life of the Parthenon Marbles as part of the story of the Parthenon is over.' The New Acropolis Museum provides compelling evidence to the contrary.
Tom Flynn is a freelance arts journalist