Iran deems "unacceptable" the Egyptian army's toppling of the country's first freely elected president Mohamed Morsi, the foreign ministry said on Monday.

"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 42 Islamist protesters demonstrating outside an elite Cairo army base against last week's ouster of President Morsi.

Iran had tried to improve its long strained relations with Egypt after Morsi, the candidate of the Muslim Brotherhood, took power in June last year.

Last August, Morsi became the first Egyptian leader to travel to Tehran since Iran's 1979 Islamic revolution.