"The intervention of armed forces in political affairs is unacceptable and disturbing," ministry spokesman Abbas Araqchi told the Mehr news agency, when asked about the developments in Egypt.
"It cannot be denied that foreign hands are at work here," Araqchi said, adding: "The polarisation of Egyptian society is dangerous."
He did not specify which foreign hands he believed were behind the coup but said: "The West and the Zionist (Israeli) regime do not want a strong Egypt."
His remarks came after gunfire killed Islamist protesters demonstrating outside an elite Cairo army base against last week's coup.
Last August, Morsi became the first Egyptian leader to travel to Tehran since Iran's 1979 Islamic revolution.