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In what could be one of the biggest counter-terrorism seizures in US history, federal prosecutors sought to take over four US mosques and a New York City skyscraper owned by a Muslim organisation suspected of being controlled by the Iranian government.

Prosecutors on Thursday filed a civil complaint in a federal court against the Alavi Foundation, seeking the forfeiture of more than $500m (£300m) in assets, including bank accounts, Islamic centres consisting of schools and mosques in New York, Maryland, California and Houston, more than 40 hectares of land in Virginia, and a 36-storey Manhattan office tower.

Confiscating the properties would be a sharp blow against Iran, which the US government has accused of bankrolling terrorism and trying to build a nuclear bomb.

Prosecutors said the Alavi Foundation managed the office tower on behalf of the Iranian government and, working with a front company known as Assa Corp, illegally funnelled millions in rental income to Iran's state-owned Bank Melli. A US Treasury official has accused Bank Melli of providing support for Iran's nuclear programme, and it is illegal in the US to do business with the bank.

John D Winter, the Alavi Foundation's lawyer, said it intends to challenge the case in the courts. He claimed that the foundation has been co-operating with the government's investigation for the better part of a year. "Obviously the foundation is disappointed that the government has decided to bring this action," he said.

The action against the Shia Muslim mosques is sure to inflame relations between the US government and American Muslims. Ibrahim Hooper, spokesman for the Council on American- Islamic Relations, said: "Whatever the details of the government's case against the owners of the mosques, as a civil rights organisation we are concerned that the seizure of American houses of worship could have a chilling effect on the religious freedom of citizens of all faiths and may send a negative message to Muslims worldwide."