The operation against an al Qaeda target resulted in the Trump administration's first combat death, Navy SEAL Chief Petty Officer William "Ryan" Owens, after Special Forces came under enemy fire.
"This was a mission that was started before I got here. This was something that was, you know, just they wanted to do. They came to see me. They explained what they wanted to do, the generals, who are very respected," he said. "My generals are the most respected that we've had in many decades I believe. And they lost Ryan."
The White House did not respond to a CNN request to clarify the meaning of Trump's comments.
Trump recalled the scene at the Dover Air Force Base where he went to meet Owens' body and said he understood why Owens' father did not want to meet with him.
"I was at the airport when the casket came in, the body came in, and it was very sad," Trump said. "I met most of the family, and I can understand people saying that."
He added, "What's worse? There's nothing worse."
Trump also repeated his defense of the mission, citing Secretary of Defense James Mattis' assessment.
"Again this was something that they were looking at for a long time doing, and according to Gen. Mattis it was a very successful mission. They got tremendous amounts of information," Trump said.
CNN has reached out to the Pentagon about Trump's comments.
The raid in Yemen occurred in late January during the second weekend of Trump's presidency. Owens died, an aircraft crashed, several service members were injured and reports have indicated many civilians were killed.
A White House official told CNN on Sunday that the mission was thoroughly vetted and planning had begun months before under the Obama administration.
The official said Mattis reviewed the operation's plans for several days and added that the ground commander decided to proceed with the mission despite knowing the team had "lost the element of surprise."
"There's risks with every military op that you take," the official said.
Colin Kahl, a national security official in the Obama administration, told CNN's Kate Bolduan earlier this month that the White House's claim that the raid was approved under Obama is incorrect.
He said Obama was never briefed on the raid and followed a recommendation to defer granting authority for raids like this until the Trump administration.
"The reality was there was never an operation or raid briefed to the Obama administration," Kahl said when asked about the Yemen raid.
In the Fox News interview, Trump also defended his use of Twitter to blast Arizona Republican Sen. John McCain for saying he didn't view the mission as a success.
"I felt badly when a young man dies and John McCain said that was a failed mission. According to Gen. Mattis, it was a very successful mission," Trump said. "And I thought it was inappropriate."