Mahathir, who returned to office in 2018, also took issue with Trump's character at a press conference, Malay Mail reported Monday.
The Malaysian prime minister said his comments were not for "all Americans," who he said were "very nice people."
"I didn't refer to all Americans. I just said with regards to President Trump only," Mahathir said. "I find that Americans are very nice people, but not President Trump. I asked him to resign to save America."
Mahathir's criticism of Trump began Saturday at the Third Conference of the League of Parliamentarians for Al-Quds. The Malaysian leader was providing his reaction to the Trump acquittal.
The U.S. Embassy in Kuala Lumpur responded to the prime minister's remarks.
"We are disappointed by Prime Minister Mahathir's comments regarding President Trump," the embassy said in statement.
"The prime minister's remarks were not in the spirit of the constructive dialogue that has long served as the foundation of U.S.-Malaysia relations.
"Throughout Malaysia's history, the U.S.-Malaysia partnership has produced outcomes important both regionally and globally, as we have cooperated on issues including security, trade, education, public health and the environment."
On Saturday Mahathir had criticized Trump's "Deal of the Century" in the Middle East. The Malaysian prime minister said Trump has legalized Israeli occupation of Jerusalem with his policy and that the move was done without consulting Palestinians.
"This peace plan only recognizes Israeli occupation and completely ignores the rights of oppressed Palestinians," Mahathir said, according to Anadolu Agency.
Mahathir also said at the conference Trump used "foreign pressure" to win the presidential election.