Mohammed Sarwar Danish, the justice minister, told reporters that the 41-year-old was released from the high-security Policharki prison on the outskirts of Kabul late on Monday.
The announcement came after the United Nations said Abdul Rahman had appealed for asylum outside Afghanistan and that the world body was working to find a country willing to take him.
"We expect this will be provided by one of the countries interested in a peaceful solution to this case," said UN spokesman Adrian Edwards.
Danish, the justice minister, said: "We released him last night because the prosecutors told us to. His family was there when he was freed, but I don't know where he was taken."
Deemed mentally unfit
Mohammed Eshak Aloko, the deputy attorney-general, said that prosecutors had ordered Abdul Rahman's release because "he was mentally unfit to stand trial".
Aloko added that deliberations on his asylum request were ongoing.
Abdul Rahman has denied that he is mentally unstable.
He told a preliminary hearing two weeks ago that he had become a Christian while working for an aid group helping Afghan refugees in Pakistan, 15 years ago.
The case provoked outrage in the US and other nations which helped to overthrow the Taliban government in 2001 and currently provide aid and military support for the Afghan president, Hamid Karzai.
George Bush, the US president, is among those insisting that Afghanistan protects personal beliefs.
The international outrage put Karzai in a difficult position as he also risked offending religious sensibilities in Afghanistan, where senior Muslim clerics have been calling for Abdul Rahman to be executed.
Several Muslim religious leaders have threatened to incite Afghans to kill him if he is freed, saying that he is clearly guilty of apostasy and deserves to die.
A group including clerics and a former prime minister said last week the government risked rebellion if it caved in to Western pressure.
About 1000 angry protesters marched through the northern city of Mazar-i-Sharif on Monday chanting "death to America" and "death to the convert Abdul Rahman".
His release is almost certain to provoke more protests.