Iran's ambassador to the United Nations, Mohammad Javad Zarif, called the plan a clear violation of a 1981 US-Iranian agreement signed at Algiers.
Under the accord, the United States pledged "not to intervene directly or indirectly, politically or militarily in Iran's internal affairs."
It is not clear whether approval of the funding was linked to Iran's presidential election in June. Iranian President Mohammad Khatami will step down after two terms in office.
But US State Department Spokesman Richard Boucher denied the charge saying the $3 million provision was made in US legislation.
"It (the allocation) is available now for educational institutions, humanitarian groups, non-governmental organisations and individuals inside Iran who would work to support the advancement of democracy and human rights. None of the activities that are mentioned are inconsistent with our commitments to the Algiers accords," Boucher said.