Comey came under fire from Democrats for sending a letter to congressional leaders shortly before the November 8 election that announced he was resuming an investigation related to Clinton's use of a private email server while secretary of state.
Clinton, the Democratic nominee, has since cited the development as a factor in her defeat by Trump, the new Republican president.
"The inauguration was such a success, and such a safety success, and we want to thank you all, because it was really a very, very special experience," Trump said earlier as he addressed those attending the reception.
He congratulated retired General John Kelly, who was in the room and had just been sworn in as Trump's secretary of homeland security.
And before summoning Comey, Trump paid tribute to Joseph Clancy, director of the Secret Service, which is tasked with protecting the president and leading presidential candidates.
"There's the man," Trump said. "C'mon. Get over here. ... From day one, I have felt safe."
Clancy got a hearty handshake.
