It couldn't be a worse day to visit what must be one of the most popular museums in the world among children. It's the first day of the Easter holidays and the Cromwell Road entrance of London's Natural History Museum is heaving.

Michael Dixon's neat, fifth-floor office is boiling in the spring sunshine. Despite being an outsider, he has quietly fitted into his role as the director of the Natural History Museum and the sector as a whole. Dixon trained in zoology at Imperial College London and then studied for his doctorate at York. His specialist area was partly on the cause of the parasitic disease bilharzia.

Dixon is keen to point out that he has all the credentials needed to run a commercial, scientific and cultural venture such as the Natural History Museum. 'There probably aren't huge numbers of people out there with that balance of skills,' he says.

No doubt the trustees made the appointment, three years ago, because of Dixon's business acumen. He cemented this while director general of the Zoological Society of London, which runs London and Whipsnade zoos.

Arriving there several years after the financial disaster that almost led to the closure of the zoos, he says there was still much to be done. 'The challenge was to put a well-known institution back on the map, knowing it had been through tough times,' he says. 'Lots of bits of the organisation were trying to coexist.'

Each zoo, and even many of the departments, were being managed separately. He brought them together as one coherent entity and introduced a new public identity.

'We made everybody think about the big picture, and what part they played and how that presented the entire organisation,' he says. The reorganisation included raising prices, as well as focusing more on retail, catering and other franchises.

Dixon admits it was a turbulent time. 'Cultural change is never easy, but there was a willingness to improve the organisation,' he says. In 2004, he left a legacy in the shape of a £10m VAT rebate, won in a landmark case.

Dixon says he could have stayed at the Zoological Society to see the completion of the aquarium planned for London's Docklands (it still hasn't happened), but he had done the big things that were going to make the difference. 'That interests me more than fine tuning,' he adds.

The Natural History Museum is trying to communicate a serious scientific message as effectively as it tells visitors about the blue whale and dinosaurs. The Darwin Centre - the first phase of which opened in 2002, two years before Dixon's arrival - is going some way towards getting across this scientific and research role.

He says the trustees hadn't committed to phase two of the project when he arrived at the museum, and he was asked to give an objective view as to its potential.

He says the concerns were about fundraising, although some of this was already in place. 'I came to the conclusion that this was a massively important project for the museum and we had gone so far with raising money, that we would have to commit our own resources if necessary to complete it.'

Dixon says he will be playing to his strengths to make a difference at the museum - and the proof of the pudding will be in its commercial performance. In the three years he has led the museum, earned income has risen 20 per cent year-on-year to £20m, as a result of working the commercial franchises harder.

There is also the matter of the museum's sister site in Hertfordshire, which has just been rebranded the Natural History Museum at Tring. It was formerly known as the Walter Rothschild Zoological Museum and Dixon says dropping the Rothschild name will allow other sponsors to come on board to help with the £800,000 a year running costs.

Dixon was interested in science - particularly biology - as a young boy. 'Science intrigued me,' he recalls. 'Questions about where we come from and how the world works appealed.'

But Dixon made a decision early on that it was business he wanted to pursue. He says he was 'not so dedicated to living on soft money', so instead of chasing the research grants and fixed-term contracts, he opted for 'more stability'. It was this leaning towards the commercial world that led him into scientific, technical and medical publishing in the 1980s.

Dixon has a straightforward, business-like manner that never lifts to reveal a smile or a laugh. Unlike other national museum directors who exude charm and charisma, Dixon is less interested in talking and posturing, and more in getting things done. He doesn't appear to be a natural schmoozer - a good thing, some might think.

He is open and finds it easy to answer questions about the challenges he has faced in his three years as head of the Natural History Museum. He tells it like it is from his standpoint, revealing much about his world view.

When I ask whether he had any doubts about holding the Steinmetz-sponsored Diamonds exhibition in 2005, Dixon says there was always a doubt. But his reservations were concerned with security issues and how they could attain the diamonds they wanted in the time they had.

The issue of conflict diamonds is controversial and Survival International, a campaigning group which supports tribal people's rights, protested outside the opening of the exhibition.

But Dixon says that part of the story was 'well exhibited' in the display, adding that Survival International's case was put on the Natural History Museum's website. As fate would have it, the exhibition opened on the day of the 7/7 London bombings and during the four months it was open - it was closed in November because of a security threat - visitor numbers suffered (half of the target 170,000 visits were reached).

Dixon and the trustees now have another high-profile case on their hands. In February, the museum found itself in the high court over the return of human remains to Tasmania.

The case was brought by the Tasmanian Aboriginal Centre (TAC), which wants the items returned immediately - the museum had agreed to return the remains, but only after scientific tests had been performed. The case is now in mediation until this month, but the stumbling block will be the scientific tests. The museum wants to extract DNA from the remains; the TAC sees this as a defilement of its ancestors.

Dixon shows little empathy towards the TAC case. 'It is a bit unfortunate that the TAC chose to use emotive language in the press,' he says.

In court, there was a suggestion that the trustees were unclear about the extent and intrusiveness of the DNA extraction process, but Dixon is bemused by this. 'You have got to understand that the majority of trustees are very senior scientists,' he says. 'We are talking about very, very small amounts of material used in that analysis. If we extract the DNA, it will go back.'

When the case is concluded, Dixon expects other indigenous groups to make similar claims, which will be judged, he says, on a case-by-case basis: 'In some situations, we envisage returning the remains to indigenous peoples, with those remains being in the care of those people but still available for scientific study. That, in my view, is a win-win.'

It is hardly surprising that Dixon is clear on the funding case for the museum, saying that although Department for Culture, Media and Sport funding is appropriate, it also undertakes contract work for other government departments, such as the Foreign and Commonwealth Office. 'We have to be more effective in getting across the message about what we are doing,' he says.

Dixon is philosophical about the poor settlement expected to come the sector's way this autumn. He believes that good past settlements from the Treasury invalidate complaints.

'We don't just go cap in hand to say give us money because we deserve it,' says Dixon. 'I think we go in a position of strength and say give us money because we are successful and demonstrably helping ourselves.'

A partnership with the United Arab Emirates is one way of showing that the Natural History Museum can look after business. It is responsible for the concept behind the Restless Planet dinosaur theme park/natural-history museum being developed as part of the Dubailand complex. There is also a possible project with Abu Dhabi in the pipeline.

Dixon says it is not simply about chasing the money - projects must fit with the museum's strategic objectives. So where does the Christmas ice-rink fit in with these objectives? Dixon makes no excuses about that being about the money. It not only generates funds, he says, but also brings in more visitors.

Ultimately, running the museum is a question of balance - raising funds while putting the science message out there.

Dixon acknowledges that one message the museum doesn't clearly spell out is what it is doing to save the planet: 'We are not yet telling people about our own green credentials,' he says. How this is communicated effectively is the issue currently exercising Dixon's grey matter.

Hoping to raise a smile, I wonder whether Dixon ever feels like throwing off his suit and replacing it with a lab coat? 'It would sometimes be nice to not to juggle a basket full of problems,' he says. 'It would be nice to look at one problem, which is what science does. But the diversity of this job is what draws me to it.'

And then he reasons that it has been a long time since he was in the lab and undertook research, so it wouldn't be 'viable for me to even try'. Perhaps not the response I expected, but certainly an earnest and direct one.