Refugees Affairs Minister Akbar Akbar lost a no-confidence vote by a large majority, while the vote for Foreign Minister Rangeen Dadfar Spanta was hanging on a single spoilt ballot.
Parliament said it would decide how to handle Spanta’s vote when it reconvened on Saturday.
Akbar has effectively lost his job but President Hamid Karzai could decide to keep him on as acting minister until his replacement is approved by parliament, MP Shukria Barakzai said.
Parliamentarians accused him of not doing enough to accommodate the thousands of refugees who have flooded into western Afghanistan after Iran said it wanted one million illegal Afghans out of its country by March 2008.
The United Nations High Commissioner for Refugees (UNHCR) says more than 52,000 were forced out between April 21 and May 8, according to government figures.
Spanta was accused of not doing enough to persuade Iran to ease its policy of forced repatriation.
At one stage eight million Afghans were living outside the country, giving it the world’s largest refugee population. Millions have returned home since the Taliban government was toppled in 2001.
Besides the one million illegal Afghans, Iran is home to 920,000 registered Afghan refugees.
Pakistan has at least two million registered Afghan refugees, which it is also trying to force home.
Spanta told the parliament Iran was piling on the pressure because of various issues including a dispute over water, with dam projects in this country likely to affect its supply.
“We are under direct pressure for signing a direct security partnership (with the United States and NATO),” he added. The US and NATO lead military forces helping the Afghan government fight the Taliban.
There have been suggestions from officials in the United States and Britain that Iran is helping the Taliban insurgents by supplying them with weapons, a claim strongly denied by Tehran.
Spanta said he had spoken to his counterparts in Iran about the claims, which they rejected.
