A US embassy statement on Friday said Washington was "concerned about unhelpful Iranian activities in Iraq".
The statement was issued a day after Iran said it accepted a proposal by an Iraqi Shia leader to talk to the US about Iraq.
Also on Thursday, Condoleezza Rice, the US secretary of state, had said she believed that US talks with Iran on stabilising Iraq would be "useful".
Iranian officials had previously said Tehran was not interested in discussions before US troops left Iraq.
Contributing to instability
America, which is leading diplomatic efforts to isolate Iran over its nuclear programme, accuses Tehran of contributing to instability in Iraq, a charge Iran denies.
Ali Larijani, nuclear negotiator and secretary of Iran's Supreme National Security Council, said on Thursday that Tehran accepted "the proposal to help resolve the problems in Iraq and establish an independent government there".
But the US embassy statement responding to his comments said: "The future of Iraq will not be decided by the United States, Iran or any other country. Iraqis will decide the future of Iraq."
"Iran's motivation is to help establishment of permanent security in Iraq and get out of suppression by the occupiers"
Ali Larijani, secretary of Iran's Supreme National Security Council
It noted, however, that a US envoy, Zalmay Khalilzad, had been authorised by the White House to enter into talks with Iran on the issue.
The Iranian foreign minister made it clear on Friday that the talks would only cover the issue of Iraq, and not Iran's nuclear programme.
Said Manouchehr Mottaki: "Our position is clear. The subject of discussions will be Iraq.
"The Islamic Republic of Iran will hold talks with the United States about Iraq to help the process of building a government there, and to support the Iraqi people."
Larijani, the nuclear negotiator, reiterated on Friday that Iran favoured a pullout by US-led forces as a step towards Iraq's full sovereignty.
"Iran's motivation is to help establishment of permanent security in Iraq and get out of suppression by the occupiers," the official Islamic Republic News Agency quoted Larijani as saying.
"We insist to have transparent talks [with Washington] and reiterate once again that we would do whatever needed to aid the sovereign Iraqi government."
Neither Iran nor the US have said where the talks would be held.