When the Pierre Bonnard retrospective moved from London to New York where it opened at the Museum of Modern Art recently two subtle, pastelcoloured paintings of female nudes were missing. Their owners withdrew the paintings after several other artworks loaned to the museum were seized in the search for Nazi plunder.

One of the collectors said explicitly that he had acted because of the ownership dispute involving two Egon Schiele paintings detained in New York after they were borrowed for a MoMA show in January. The Schiele paintings, on loan from the Leopold Foundation in Austria, are being held in New York while the district attorney's office carries out a criminal investigation.

The absence of two Bonnard paintings is the latest sign of alarm in the art world over works with a Nazi-clouded past. The missing paintings, Grey Nude in Profile and Standing Nude were on view when the exhibition showed at the Tate Gallery in London.

United States museums now dread the possibility that other collectors will refuse to lend European paintings in case they are seized during international shows. "When lenders see what happened to the Schiele paintings it makes them nervous, even if they haven't any reason to doubt their artworks," said Elizabeth Addison, Deputy Director for Communications at MoMA. "The potential that something could happen is enough."

Since the collapse of Communism, Eastern European families, in particular, have been actively pursuing the trail of artworks confiscated during the second World War. A Hungarian Jew, Gabor Bedo, whose father, Rudolf, sent his £5 million art collection to London for safekeeping during the war, lodged a compensation claim against the British government last month. Rudolf Bedo's collection of 150 paintings included a Renoir stilllife and a landscape by the 17th century Dutch master, Jan van Goyen. He was just one of thousands of Jews who lodged property and accounts in Britain during the second World War.

But the Trading with the Enemy Act allowed the UK authorities to freeze the property of all residents of enemy or enemy-occupied countries. The British government sold Bedo's collection at auction in 1955. A scientist with a passion for art, Rudolf Bedo survived the war but lost his sister in Bergen Belsen concentration camp. Mr Bedo died in 1978, before the Communists fell and he had the opportunity to pursue a claim for the art collection.

The British government promised earlier this year to repay assets confiscated from Nazi victims. Lord Archer of Sandwell, a former chairman of Amnesty International, was appointed recently as independent assessor to compensation claims against the UK government. Bedo's case could open the floodgates for many other compensation demands.

The subject of wartime plunder has become such a hot issue in the art world, some of the world's leading museum directors have also got together to form a task force. Earlier last month, the Association of Art Museum Directors held a brainstorming session to come up with new guidelines on how to deal with stolen artworks.

Under the chairmanship of Philippe de Montebello, director of the Metropolitan Museum of Art in New York, the group urged museums to review their collections to establish if any works were unlawfully confiscated by the Nazi regime.

The task force called for the creation of computerised research files to cross-reference claims and stolen works of art. Institutions were asked to scrutinise the origins of artworks before purchasing them or accepting them as gifts.

In recent years many second World War documents have been declassified, allowing art experts more information about the ownership of European artworks. But some curators are worried that they will become over-burdened with research into the provenance of artworks. This could reduce the amount of European works available to international audiences.

Philippe de Montebello stressed that museums are "committed to acting swiftly and proactively to conduct the necessary research that will help us learn as much as possible about works for which full ownership records previously have not been available."

For decades, US museums have counted on federal or state laws that protect art loans from detention or seizure. But a New York district attorney claimed that state law did not shield artworks under criminal investigation, when he ordered MoMA to detain the Schiele paintings instead of returning them to Vienna.

MoMA had received two letters from Jewish families claiming that the Schiele paintings were stolen or misappropriated from their rightful owners when the Nazis annexed Austria (1938-1945).

Henry Bondi wrote that his aunt, Lea Bondi, owned Portrait of Wally when Nazi collaborators took the painting from her apartment without her consent. Lea Bondi died in 1969, having attempted three years earlier to recover the painting.

Rita and Kathleen Reif, relatives of Fritz Grunbaum, stated that the painting Dead City III was taken from Grunbaum's collection without his consent by Nazi agents or collaborators after his arrest in Austria. He later died in the Dachau concentration camp.

A New York district attorney is now investigating claims that the works made their way improperly into private collections after the second World War. Last month a US court ruling said that the Museum of Modern Art could return the two borrowed Egon Schiele paintings despite a continuing criminal investigation into their ownership. But the New York district attorney examining the charges is appealing the decision. Art world experts predict that it could be a long time before the works are returned to Austria, even if the court decision is upheld.

The leading international museums rely on borrowing paintings from overseas to present first-rate shows. But the issue of art stolen during the Holocaust is provoking changes in policy. "I do think that everyone is becoming much more sensitised to this issue and most museums are taking extra precautions with their own collections. At MoMA, we are doing research on all works from this historic period, says Addison.

MoMA breathed a sigh of relief when the Netherlands decided not to contest a claim to a painting by Vincent Van Gogh recently left to the museum by a private collector. The Dutch government says it has a right to Olive Trees, estimated to be worth around £21 million pounds. But the Dutch authorities said that they would not demand the painting's return to set an example and avoid a circus of claims and counterclaims.

Other institutions are taking new measures to protect their collections. Before the Metropolitan Museum of Art, New York, shipped three dozen works by Paul Klee to an exhibition in Berlin recently, museum officials wrote to German museums asking if they had any claims on them. In Washington, the US State Department is now assessing whether new regulations are needed to protect international cultural loans from seizure.

Ethical problems surrounding paintings confiscated by the Nazi regime threaten the free flow of art work across the Atlantic. But the world's top museums cannot afford to turn a blind eye to stolen art.