"The marriage of people of the same sex is not possible in Italy," the centre-right minister said on Tuesday. "So these marriages cannot be recorded in Italian registries... for the simple reason that the law doesn't allow it."
He said he had circulated orders to municipalities across the country to "cancel" the records, or he would do so personally.
The response was swift from several city halls that recognize gay couples who married abroad.
"If they want to cancel (them), let them, but not in the name of Bologna," said the northern city's mayor, Virginio Merola. "I will not obey."
"To send out a circular on questions that concern the daily life of so many people is not only bureaucratic but tragicomic," said the mayor, a member of the centre-left Democratic Party who has allowed the transcriptions since mid-September.
In Rome, deputy mayor Luigi Nieri commented: "Angelino Alfano can't manage to concentrate on preventing crime, on security, on fighting the mafia – in short on the duties of the interior minister. He has other priorities, but I will fight for the transcription of homosexual marriages in Rome."
Similar reactions came from the cities of Udine and Naples, while the consumer group Codacons dismissed the step as "illegitimate" because it "clearly violates the decisions of the European Court of Human Rights on free unions."
“A question such as this will not be resolved with bureaucratic circulars, but must be taken to parliament or before the Constitutional Court,” said Udine’s mayor Furio Honsell.
Trieste and Florence are among other Italian cities that recognise same-sex marriages from other jurisdictions.
However, some mayors spoke out in support of Alfano with Umberto Di Primio, the mayor of Chieti saying that Alfano had “made the right decision”.