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Trump made the comments on "Fox & Friends" when he was asked if Holt "leaned a little over into the left lane" Monday night.
"Yeah, totally. More than a little," Trump replied. "He leaned over in that lane."
The Republican presidential nominee expressed disappointment that Democratic nominee Hillary Clinton was not asked about issues that are unflattering to her candidacy.
"Well, he didn't ask her about the emails at all. He didn't ask her about her scandals. He didn't ask her about the Benghazi deal that she destroyed," Trump said, referring to the 2012 terror attack on the US diplomatic compound in Libya. "He didn't ask her about a lot of things that she should have been asked about."
The brash billionaire continued:
"I mean there's no question about it. He didn't ask her about her foundation. Why? I don't know. I didn't think he did a bad job, but when you look at it you watch the last four questions. He hit me on birther, he hit me on a housing deal from many years ago that I settled with no recourse and no guilt. He asked me about that, that's a beauty to be asked. A 40 year old lawsuit or older. I just hate to say its older because then Ainsley will say wow I didn't know Trump was that old. She'll be unimpressed. I explained it, but when you explain that it is a no win too. They were leaving all her little goodies out. They didn't ask her about much. I was asked about my tax returns which I've told about 500 times. I think I really did well when we were asked normal questions. I think I did really well when answering those questions, but those questions are not answerable in a positive light."
Trump initially told CNN after the debate that Holt did "a great job."
"Honestly, I thought Lester did a great job," Trump told the media outlet in the spin room. "Yeah, I thought it was very fair."
Mike Pence, Trump's running mate, also said on Tuesday he was "disappointed" in Holt's performance. Speaking on "Good Morning America," the Indiana governor said he wished Holt brought up some of the scandals that have been "at the forefront" of Clinton's campaign.
Holt's performance first came under scrutiny from far-right websites like Breitbart, which published articles knocking the "NBC Nightly News" anchor for fact-checking Trump and not pressing Clinton on her use of a private email server as secretary of state.
Former New York City Mayor Rudy Giuliani, a prominent Trump surrogate, also told reporters after the debate that Holt "should be ashamed of himself" for the way he navigated a discussion about so-called stop-and-frisk policing tactics.
Some conservatives, however, praised Holt's performance, and the reviews he received were mostly positive.
Monday's debate at Hofstra University was the first of three debates set to take place before voters cast their ballots in November.