The leaked emails included passages in which Lord Mandelson told Epstein to “fight for early release” shortly before he was sentenced to 18 months in prison.
He is also reported to have told Epstein “I think the world of you” the day before the disgraced financier began his sentence for soliciting prostitution from a minor in June 2008.
Speaking to reporters, Sir Keir said the messages showed Lord Mandelson “was not only questioning but wanting to challenge the conviction of Epstein at the time”.
Lord Mandelson’s emails “cut across the whole approach that I’ve taken on violence against women and girls for many years and this government’s”, he added.
The emails showed “the nature and extent of the relationship that Peter Mandelson had with Epstein was far different to what I had understood to be the position when I appointed him.”
Sir Keir added he was “not at all” satisfied with Lord Mandelson’s responses to questions “put to him by government officials”.
The prime minister has faced questions about his judgment in appointing the peer, whose friendship with Epstein was public knowledge, in the first place.
The scandal, coming so soon after Angela Rayner’s resignation as deputy prime minister, has encouraged some Labour MPs to become more vocal about their frustrations with the prime minister’s leadership and the wider Downing Street operation.
Sir Keir insisted he did not know what was in the emails when he defended the US ambassador at PMQs but said he knew Foreign Office officials had asked Lord Mandelson questions about the email.