The two Irish diplomats accused of having talks with Taliban militants flew out of Afghanistan after negotiations to stop them being expelled failed.
The Afghan government ordered the two senior diplomats, one who works for the UK government, to leave after accusing them of being "detrimental to the national security of the country".
Reports say the pair left Kabul early this morning after two days of talks failed to prevent the expulsion.
The British Foreign Office refused to comment on the matter saying it was a matter for the United Nations and the EU.
Michael Semple, deputy head of the EU mission in Kabul, and Mervyn Patterson, a senior UN official understood to be a British citizen from Northern Ireland, visited the volatile southern province of Helmand on Monday.
Mr Semple's position is funded by the State.
The UN said they talked to people on the ground there but strongly denied that this included Taliban militants.
But Afghan president Hamid Karzai's spokesman, Humayun Hamidzada, claimed the two were involved in activities "that were not their jobs".
Aleem Siddique, a spokesman for the UN mission in Afghanistan, described the situation as a "misunderstanding" but said both men had agreed to leave the country today.
"We see no basis for such a decision but we respect the sovereignty of the government of Afghanistan and have every intention to abide by that decision," he said.
"We are hopeful to get their return as soon as possible." Mr Siddique added:
"There is a miscommunication between the authorities in Helmand province and the central government, and that's what we're trying to clear up. "We don't talk to Taliban, full stop."
Both men have worked in Afghanistan for many years, speak local languages fluently and understand the country's complex tribal structures.
The diplomatic row follows claims the British secret service has itself held secret peace talks with senior Taliban insurgents.