"We are skeptical that such a just solution can be found in the arrangement announced," State Department spokeswoman Victoria Nuland said.
She denounced "Iran's record of cooperation" with international bodies as "profoundly deficient," saying that also raised concerns about whether Tehran would "be focused on achieving justice promptly."
Israel has already protested the accord reached with Iran, summoning Argentina's ambassador on Tuesday to complain about the decision.
But Argentine President Cristina Kirchner, who announced the deal Sunday, said the agreement may allow Argentine authorities to finally question suspects currently the subject of Interpol "red notices."
Argentina has long accused Iran of masterminding the deadly attack, in which 85 people were killed, and since 2006 has sought the extradition of eight Iranians, including current Defense Minister Ahmad Vahidi and former president Akbar Hashemi Rafsanjani.
Washington's position on the bombing "remains unchanged," Nuland said, adding "the Iranian government has a responsibility to cooperate fully with Argentine authorities in seeing that the perpetrators are brought to justice."