Davide Zotti, a philosophy teacher in a state school in Trieste, said he had taken down the crucifix to protest the "homophobic statements" of the Catholic Church.
"I exercised by right and my duty to defend the secular nature of the state I work for," he wrote on his Facebook page.
School management saw his action otherwise, ordering the reinstatement of the crucifix and giving Zotti an official warning about his conduct.
Catholicism has not been Italy's state religion since 1984 but an order dating from Benito Mussolini's reign requiring the presence of crucifixes in schools has never been revoked.
"It is stupefying that, in 2014, a state school cannot find a better way of imposing the crucifix than resorting to a fascist rule," Italy's Union of Rationalist Atheists and Agnostics (UAAR) said in a statement on the case.