In testimony Thursday to the House Government Reform Committee, a White House aide acknowledged that he asked that employees keep quiet about the difficulties, but said he never threatened anyone.
"I did say ... that this was a matter that I believed that needed to be kept in bounds with those people who needed the information to perform repairs to the system," Mark Lindsay testified. Lindsay said he didn't want people "talking around at the water cooler."
Details of the massive problem are only now emerging, while a Justice Department court filing revealed that prosecutors have launched a criminal investigation to learn what happened. Many of the e-mails apparently hidden from congressional and Justice Department investigators were Vice President Al Gore's messages on campaign fund raising.
Charles Ruff, who was the White House counsel in 1998, and John Podesta, deputy chief of staff at the time, were told about the breakdowns in internal memos that year.
"This memorandum is to advise you of an anomaly in the system in the Mail2 server, which primarily supports the day-to-day e-mail traffic of the White House Office ... ." Podesta was informed by another presidential aide on June 19, 1998. Podesta is now the president's chief of staff.
In prepared remarks, Beth Nolan, the current White House counsel, told the House committee that after Ruff and Podesta were told of the problem, they thought it had not affected law enforcement and committee's subpoenas.
"Thus, as Mr. Ruff understood the technical problem at the time, he did not think that the error had an effect on previous searches or that it might affect future searches of e-mail records," Nolan said. "As a result, Mr. Ruff had no reason to believe there was any need to notify investigative bodies of this error."
Another internal White House memo on Sept. 4, 1998, showed that computer officials were aware of problems "regarding OVP (Office of the Vice President) e-mail and records management." The memo laid out the problem in technical terms, but there was no indication it was discussed with Gore's staff.
Nolan told the committee, however, "It appears that much, if not all" of Gore's e-mails were not captured by the White House archive system. But she said officials were reviewing backup tapes from the vice presidential e-mail system to see if any of them can be reconstructed.
White House spokesman James Kennedy said some of the Gore e-mails may have been found and provided to investigators after searches of files of officials who sent or received the vice presidential messages.
The archive failure was Nolan said, explaining that Gore's office simply used a different e-mail system that until 1997 could not be archived by the normal White House system.
The criminal investigation will be conducted by the campaign fund-raising task force which had subpoenaed the e-mails as part of its overall investigation into fund-raising abuses in the 1996 election.
The controversy spilled into the presidential campaign. Republican George W. Bush said Thursday, "This is a White House that needs to let the sunshine in when it comes to campaign funding allegations. I look forward to seeing where those e-mails are, and what was in those e-mails."
Some private sector contract employees, who were hired by the White House to work on the e-mail system, contended they were threatened by White House officials with termination and even prison if they told anyone about the breakdown. Those allegations will be reviewed in the criminal probe, the Justice Department said.
The department revealed the investigation in papers filed in a civil lawsuit brought by individuals who contend the White House improperly obtained and misused their FBI background files. The plaintiffs sought e-mails related to those files.
The Justice Department asked a federal judge for more time to answer that demand, contending any response now could jeopardize the criminal investigation.
The delay was called a "ploy" by Larry Klayman of Judicial Watch, the conservative legal organization that filed the $90 million class action suit.
"This is not the first time the Clinton-Gore Justice Department used its campaign finance task force as an excuse to try to take evidence away from the court," Klayman said, adding he would oppose the delay and seek court sanctions if the deadline is not met.