Tony Fratto, the White House spokesman, said there was no reason to believe the emails had been deliberately destroyed.
But rights groups said the issue raised concerns over the administration's handling of public records.
In addition, although the recycling process ended in 2003 - two years after Bush first entered office - some emails from 2003 to 2005 may also not have been fully preserved, Payton said.
The White House started preserving back-up tapes in October 2003, shortly after the start of the investigation into who leaked the identity of Valerie Plame, a CIA operative, in July that year.
Plame's identity was leaked after her husband, Joseph Wilson, wrote a New York Times piece condemning the Bush administration for claiming that the Iraqi government under Saddam Hussein, then Iraqi president, was buying uranium from Niger.
The claim was proved to be false, however it featured in Bush's 2003 state of the union address.
Two federal statutes require that presidential communications, including emails from senior White House aides, must be preserved for the nation's historical record.
White House condemned
Rights advocates say that emails from crucial periods in Bush's first tenure in office could now be lost, including emails from the period when the US was at war in Iraq.
"They didn't have what any archival person would consider to be an electronic record-keeping system," Anne Weismann, chief counsel for the ethics group Citizens for Responsibility and Ethics in Washington (CREW) which is one of the groups suing over the emails, told the Washington Post newspaper.
"These are not the steps of a White House committed to preserving records or meeting its obligations under the law."
However Fratto said there was "no basis" to say that the the White House had destroyed any evidence or "engaged in any misconduct" and criticised the organisations for "inflammatory" accusations.