Whether it is online galleries such as Charles Saatchi's Your Gallery or internet art such as jodi.org, created in 1995 by Joan Heemskerk and Dirk Paesmans, digital technology is turning the contemporary art world upside down. New media artworks no longer need to be seen within the confines of a gallery or museum but can be viewed by a global audience over the web.

For museums, this raises many questions. For a start, the internet gives artists the means of production and distribution. 'It's the beginning of a new era, which is fantastic in terms of the growing independence and power of the individual artist,' says David Ross, who built up the Long Beach Museum of Art's video collection in the 1970s and was later a director of the San Francisco Museum of Modern Art.

'You can click on the website of artist X and bookmark it - and if there's a box for using PayPal, you can give him a buck, and if 20,000 people around the world do that, that person has made $20,000 for a work he's never had to distribute except on his own server.'

Yet while artists branch out into cyberspace, bricks and mortar institutions have been setting up new departments, hiring curators and staging retrospectives of video art as new media is given serious attention by even the most conservative organisations.

At the end of last year, New York's Museum of Modern Art (MoMA) created a department of media and hired Klaus Biesenbach as its chief curator. Also last year, the UK's National Museum of Photography, Film and Television in Bradford changed its name to the National Media Museum to reflect the changing landscape.

In 2005, the Getty Research Institute acquired the Long Beach Museum of Art's collection (the US's largest video archive) of more than 5,000 works and related documents by artists who use digital media such as Bill Viola, Eleanor Antin, Bruce Nauman and Paul McCarthy.

These institutions believe that, with an overwhelming amount of new material being created, they play an essential role in selecting and collecting the most important works.

But this is no easy matter, particularly when it comes to what is on the internet. 'There's a massive diversity of websites out there,' says Paul Goodman, the head of collections at the National Media Museum. 'So which pages do we grab that are representative, or should we be comprehensive?'

Also, for some of the new art, the web is meant to be the sole channel for viewing. 'Is a screen grab going to tell everybody what they need to know?' asks Goodman. 'And what capacity do we need to store these screen grabs?'

Preserving the newest material is not the only challenge. Much video art is several decades old and some works are deteriorating. In response, several institutions have embarked on major conservation efforts. The Getty Research Institute is expanding its facility for audiovisual conservation and has been logging works and preparing items for scholarly research and public viewing.

The New Art Trust - in partnership with Tate, MoMA and the San Francisco Museum of Modern Art - is bringing together curators, conservators and technicians to establish guidelines for the care of electronic art such as video, film, audio and computer-based installations. It aims to develop internationally agreed standards for the handling, installation and conservation of such works.

But while preserving and cataloguing the works themselves is one thing, maintaining the hardware needed to present them is another. Conservation work therefore includes safeguarding projection equipment and video players, cataloguing each machine and the work for which it was intended and preserving operator manuals, sources for spare parts and details of repairs.

Even so, equipment that was made in the 1970s may become unusable once spare parts are no longer available. Betamax video and other technologies have given way to CD-Roms and DVDs - and the pace of technological change will only accelerate. 'There are already certain works that you have to restore and transfer [on to new formats] because otherwise in a couple of years they would be lost forever,' says MoMA's Biesenbach.

Yet transferring art from a medium such as film negatives to a digital format can change colours, textures and tones. The challenge for curators is how to do so while remaining faithful to the artist's original intention.

'If we're changing the hardware that it's played on in the future, are we altering what it was like originally? And that's against what conventional museum wisdom is about in terms of maintaining the historical integrity of an object,' says Colin Philpott, the head of the National Media Museum.

Philpott believes it is essential to maintain relationships with technicians and make sure that 'at the very least we keep some of the original hardware to demonstrate how it was originally engaged with by the public'.

Curators and experts also agree that collaboration with the artists themselves is crucial. 'The best museum practices today are about establishing in writing from the artist a detailed description of the look and feel of these works so that curators will be able to interpret, based on the descriptions by the artists, precisely how those works should look,' says digital art expert David Ross.

This is also true for new media installations. Take Sleepwalkers, the cinematic artwork by Doug Aitken displayed at MoMA earlier this year. Eight continuous sequences of film were projected on to the exterior walls of the museum. Such works are complex to install and not easily moved to other institutions.

Nevertheless, Biesenbach insists that such works can and should travel. 'Even this work will be moveable,' he says. 'One of Doug's most important pieces, Electric Earth, was created for the Venice Biennale in 1999, but then a year and half later it was in the Whitney.'

Again, collaboration with artists is crucial when moving their pieces from one space to another. But there will come a time when the artists will no longer be around. When this is the case, individual interpretations of the presentation and conservation of video and new media artworks may start to receive critical attention.

This is nothing new. 'The conservation of paintings of the 1500s and the way in which conservators bring back a picture to life is also incredibly controversial,' says Ross. 'Critics denigrate or celebrate museums for the kind of work they do in bringing a picture back to life.'

In any case, few artworks are seen in their original context. In Rembrandt's time, the spaces in which people viewed art were quite unlike those in which it is now seen, says Wulf Herzogenrath, the director of Kunsthalle Bremen, whose new media department presents audio, video, photographic and computer art and installations.

'There was no electric light, there was no white cube - it was shown in a dark room of someone who smoked cigars,' he says. 'It was a very different light that Rembrandt was thinking of - he couldn't imagine the beautiful light we have in museums.'

For Herzogenrath, technological considerations are secondary. 'We have to discuss it in the way we discuss the difference between acrylic painting and oil painting or, with the pencil, we compare the H9 and the H3,' he says. 'But it's not the hardware that's interesting. It's what the artist has done with the image, the time, the rhythm, the sound.'

For this reason, Herzogenrath believes that the role of the museum has not altered, despite the changes in media. 'We own and select and present,' he says. 'This is because the public wants to see the 50 most interesting works - they don't want to see one million works.'

Ross agrees: 'The core value and purpose of the traditional art museum doesn't really change. The museum's primary goal is to preserve educate and collect so that great examples of great art exist in perpetuity. That's a serious mission and it doesn't change.'

Sarah Murray is a freelance journalist based in the US