Campaign groups Citizens for Responsibility and Ethics in Washington and the National Security Archive filed requests in May for copies of emails from the White House relating to a number of issues, including the planning for the war in Iraq.
The White House has been fighting the case ever since and has now claimed that it cannot comply as the emails have been lost.
A court has now given the Executive Office of the President until 5 May to come up with a full account of its data backup strategy, and to clarify the status of backup tapes covering March 2003 to October 2005.
White House staff have offered contradictory claims that backup tapes have been overwritten.
"The court is reacting to the inconsistencies in the White House statements, " said Meredith Fuchs, general counsel at the National Security Archive.
"Emails are lost one day, the next they are not. Emails are recoverable, then they are not. Backup media is saved, then it is not.
"What worries us is that time is passing. There are only eight and a half months until this administration leaves office.
"If nothing is done soon not only could the emails disappear for good, but the federal records that are commingled with the presidential records could get swept away and become inaccessible for the next 12 years."
Some have questioned how it is possible that so many emails have gone missing from a government department.
The Executive Office of the President has previously said that the losses occurred while switching from Lotus Notes to Microsoft Exchange when staffers were left to decide what to archive and what to delete.
"Given the technological advances of today's society, it seems a little archaic to leave the archiving of potentially sensitive and highly classified information in the hands of the end user, particularly for an organisation so firmly in the public spotlight," said Juergen Obermann, chief executive at archiving specialist GFT Solutions.
"While this throws up some serious concerns over internal policy it is more worrying that, by failing to archive all correspondence, the very body supposed to be upholding the law is clearly in violation of it."
White House 'loses' five million emails
By Iain Thomson on May 3, 2008 1:19PM