"It is natural that as long as a fatwa has not been annulled, it is still valid," foreign ministry spokesman Hassan Ghashghavi said at a news conference suggesting that Khomeini's order was still valid.
The Indian-born Rushdie, 61, was forced to go into hiding for a decade after Khomeini issued the 1989 death sentence over his book "The Satanic Verses," saying it insulted Islam.
Khomeini's successor as supreme leader, Ayatollah Ali Khamenei, said in 2005 he still believed the British novelist was an apostate whose killing would be authorised by Islam.
Iran accused Britain of Islamophobia in 2005 when it awarded Rushdie a knighthood.
