Mike McCurry, the President's chief spokesman, said that while the relationship may have been "simple" and "innocent" it had probably been "very complicated".
Mr McCurry added that sooner or later Bill Clinton would have to provide a full account of what exactly had transpired between himself and the former White House intern, who allegedly told a friend on tape that she had an affair with the President when she was 21.
The President has denied having had an "improper" or "sexual" relationship with Ms Lewinsky but, in an interview published in yesterday's Chicago Tribune, Mr McCurry acknowledged that something had gone on.
"Maybe there'll be a simple, innocent explanation," he said. "I don't think so, because I think we would have offered that up already."
Mr McCurry, who had previously insisted that he was in the dark as to the details of the Lewinsky affair, said the President had been hesitant to reveal more for fear of providing his enemies with the opportunity to twist the truth.
"We are not in a position to provide a full and complete account, so the art is to make sure everything we say is truthful and credible," said Mr McCurry, offering a glimpse of the calculated manipulation of public perceptions of which he has been a part.
As for his own, personal, apparently less varnished view of what the truth might be, Mr McCurry said: "I think it's going to end up being a very complicated story, as most human relationships are. And I don't think it's going to be entirely easy to explain, maybe."
But he did say that allegations that Mr Clinton had sex in the Oval Office where "pretty implausible" because there was "so much traffic" in and out of the President's office.
On the face of it, Mr McCurry's statements smack of treachery. His boss, backed up forcibly by Hillary Clinton, has flatly denied having had an affair with Ms Lewinsky.
But now Mr McCurry, the President's hitherto loyal lieutenant, is openly venturing the view that the relationship may not have been "innocent".
He is also suggesting it may not be "entirely easy to explain" and, perhaps most damning of all instead of squarely endorsing the President's denial of a sexual relationship, Mr McCurry is prepared to go no further than to say that the notion of illicit sex in the Oval Office is "pretty implausible" - a remark open to the interpretation that sex in some other White House chamber may have been less implausible.
It could be that Mr McCurry, who wanted to leave the President's employment a year ago but succumbed to pressure to stay on, is heartily fed up of enduring the daily indignity of responding to reporters' questions with evasions and half-truths.
He may have seen the interview with the Chicago Tribune as an opportunity pre-emptively to distance himself from any unseemliness that might emerge once the truth about the Lewinsky affair is finally known. An alternative explanation might be that Mr McCurry's remarks were artfully constructed in consultation with the President and his advisers, in which case the suggestion would seem to be that Mr Clinton is seeking to prepare the public for revelations that in some way deviate from the forceful denials he has issued so far.
Whatever Mr McCurry's agenda may be, it does appear to anticipate the likelihood that Ms Lewinsky will be obliged to give her version of events before the Grand Jury soon, possibly this week.
According to all the indications so far, Ms Lewinsky will sooner or later reveal that the relationship with the President was far from innocent, and very complicated indeed.