Trump said Haley, who was South Carolina governor when Trump tapped her for the UN position, told him six months ago that she wanted to take some time off.
Speaking to reporters in the Oval Office, he praised her as having done an incredible job and said he hoped she could come back to the administration in another capacity.
“We’re all happy for you in one way, but we hate to lose (you). ... Hopefully, you’ll be coming back at some point. Maybe a different capacity. You can have your pick,” Trump said.
Earlier this year, Haley, 46, told Reuters that, “Every day I feel like I put body armor on,” to protect US interests at the United Nations.
Noah Bookbinder, executive director of Citizens for Responsibility and Ethics, said: “By accepting gifts of luxury private flights, Ambassador Haley seems to be falling in line with other Trump administration officials who are reaping personal benefits from their public positions.
“Our ethics laws are clearly written to prevent even the appearance of corruption and improper influence.”
Haley is the latest in a long list of senior staff members to leave the Trump administration, including former Secretary of State Rex Tillerson, who was fired in March.
A former governor of South Carolina who is the daughter of Indian immigrants, Haley is seen as a rising star in the Republican Party and a possible candidate for the 2020 presidential elections.
But she said on Tuesday she would not be running in 2020 and would campaign for Trump.