Four IAEA inspectors left their hotel on Thursday morning and headed for the airport, the agency said.
North Korea announced on Tuesday it was ceasing all cooperation with the UN nuclear watchdog and pledged to restart work at its Yongbyon reactor. The move, and Pyongyang's withdrawal from six-party talks on its nuclear program, came in response to UN condemnation of its launch of a rocket on April 5.
The UN Security Council said on Monday the North's rocket launch contravened a UN resolution passed in late 2006 after Pyongyang's nuclear test that banned nuclear and ballistic missile activities.
North Korea's official KCNA news agency said in a statement that the UN decisions were an infringement of its sovereignty, and pledged to "bolster its nuclear deterrent for self-defense in every way."
The U.S. State Department confirmed on Wednesday that its inspection team, completely separate from the IAEA mission, had also been told to leave, and preparations for departure were underway.
The international inspectors had been overseeing the dismantling of the Yongbyon nuclear facility, in line with a February 2007 deal between the six countries involved in talks on the North Korean nuclear problem - the United States, Russia, China, Japan, and North and South Korea.
Many countries suspect that North Korea's April 5 rocket launch was a test of a long-range missile.
North Korea claimed the rocket, which was launched over Japan, successfully delivered a communications satellite into orbit, but the U.S. and South Korean militaries said all three stages fell into the ocean and that "no object entered orbit."
China and Russia used their vetoes to prevent the UN Security Council from passing a harsher resolution against the North, but joined other members in condemning the rocket launch and demanding that existing sanctions be enforced.