The order by U.S. Magistrate Judge John Facciola comes amid an effort by the White House to scuttle two lawsuits that could force the Executive Office of the President to recover any e-mail that has disappeared from computer servers where electronic documents are automatically archived.
Two federal laws require the White House to preserve all records including e-mail.
Facciola gave the White House five business days to report whether computer backup tapes contain e-mails written between 2003 and 2005.
The time period covers the Valerie Plame affair in which at least three presidential aides were found to have leaked Plame's CIA identity to the news media.
"Do the back-ups contain the e-mails said to be missing?" Facciola asked.
In a four-page order, Facciola said he needs to know "if the missing e-mails are not on those back-ups."
Facciola noted the importance of acting quickly since e-mails that might be retrievable from individual computer workstations in the White House "are increasingly likely to be deleted or overwritten with the passage of time."
White House spokesman Tony Fratto declined comment while reviewing the magistrate's order. In the past, the White House has said there could have been some e-mails that were not automatically archived because of a technical issue.
In their lawsuits, the National Security Archive and Citizens for Responsibility and Ethics in Washington suggest the e-mails were improperly deleted from White House computer servers. Over 5 million White House e-mails are missing, CREW alleged. Recently, the group said it has been told by reliable sources that the actual figure of missing e-mail is over 10 million.
In asking that the complaints be dismissed, the Bush administration says the president's record keeping practices under the Presidential Records Act are not reviewable by the courts. Also, the Federal Records Act does not allow the far-reaching action the two private groups are demanding, the administration contends.
Two months ago, the two private groups focusing on issues of government secrecy obtained a court order directing the White House to preserve the backup tapes.
The Bush administration had offered to have the government file a sworn declaration stating that the White House is safeguarding all backup materials. Instead, Facciola recommended that the judge in the case, Henry Kennedy, issue a court order because "a declaration is not punishable by contempt. In other words, without such an order, destruction of the backup media would be without consequence." Kennedy did as Facciola suggested.
The subject of missing White House e-mail arose early in 2006 when the prosecutor in the Plame investigation, Special Counsel Patrick Fitzgerald, disclosed that not all electronic message traffic of the EOP and the office of Vice President Dick Cheney "for certain time periods in 2003" was preserved through the normal archiving process.