President Mohammed Khatami has called for an "immediate end" to the strikes.
Foreign Minister Kamal Kharrazi said Iran did not approve of the US-led action, that its aims were unclear and that it would be wrong for foreign powers to impose a new government on Afghanistan.
However, Iran welcomed the Northern Alliance's capture of Kabul as a victory for the Afghan people over the Taleban, which Tehran has always opposed.
With UN support, Iran says the former Afghan President, Burhanuddin Rabbani, should play role of transitional government and pave way for broad-based coalition.