The two imams, who were not named, work at the mosque managed by the Islamic Cultural Foundation of Geneva, which is near the United Nations compound and the headquarters of other international organizations.
The two live in the French border town of Ferney-Voltaire, according to Swiss media reports.
In a statement, the foundation confirmed the search overnight Wednesday by authorities in France's Ain department.
The statement said that following the search, "the authorities gave a signed document to the two imams which attested that no object was found that could lead to a prosecution."
Police were not immediately available to comment on the search, including whether such a signed letter had actually been produced.
The foundation said that it "will make the necessary arrangements with the Geneva and French authorities to shed light on the reasons for the search."
In August, Swiss media reported that two or three imams based at the Geneva mosque had raised alarms among French national security officials.
On Thursday, a former spokesman for the mosque, Hafid Ouardiri, told the Tribune de Genève newspaper that a climate of "radicalisation" existed at the religious centre.
He told the paper that some of authorities at the mosque held "extremist" views.
The Geneva mosque was inaugurated in 1978 by the former king of Saudi Arabia, Khaled Ben Abdulaziz.
The development emerges after German-language media have identified a mosque in Winterthur in the canton of Zurich as being linked to a cell of Isis, the Islamic State group.
An official has denied the reports while a Libyan imam from the mosque, who said he is not involved with Isis, this week decried inaccurate reporting about him and the mosque.