Haley's comment came a day after Trump accused Pakistan of giving nothing to the US but "lies and deceit" and providing "safe haven" to terrorists in return for $33 billion aid over the last 15 years.
Speaking to reporters at a news conference at the UN headquarters in New York, Haley alleged Pakistan of playing "double-game" with the US for years.
"The president is willing to go to great lengths to stop all funding from Pakistan as they continue to harbour and support terrorism," said Haley.
"Pakistan has played a double game for years. They work with us at times, and they also harbour the terrorists that attack our troops in Afghanistan. That game is not acceptable to this administration," she said.
The US has also announced that it is withholding its $255 million military aid to Pakistan.
"The decision to block aid is connected to Pakistan's harbouring of terrorists," the top American diplomat said.
Pakistan has expressed "deep disappointment" over the allegations, saying the accusations strike with "great insensitivity" at the "trust" between the two countries.
Pakistan's Foreign Minister Khawaja Asif in a tweet challenged Trump's claim that the US has given Pakistan more than $33 billion dollars as aid over the last 15 years, saying verification by an audit firm would prove the US president wrong.