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.