The Basilica of San Lorenzo in Lucina is one of the oldest Christian churches in Rome and is known for a marble bust of the last Italian king, Umberto II, who went into exile in 1946.
Above the bust is a fresco of two angels, which were not particularly known before the restoration.
Now, however, one of them bears an unusual likeness to Meloni, who leads the Brothers of Italy party.
According to a report in La Repubblica newspaper on Saturday, the restorer, Bruno Valentinetti, has long had ties to the Italian conservative movement.
The winged "angel Meloni" is holding a scroll showing the boot-shaped outline of Italy, while the second angel is handing a crown to the disgraced ruler.
"There is indeed a certain resemblance," the priest of the basilica, Daniele Micheletti, told the ANSA news agency.
"But you would have to ask the restorer why he did it that way. I don't know."
Valentinetti, however, said he sees no resemblance to the Italian leader, emphasising that he had only "restored what was already there 25 years ago".
La Repubblica said Valentinetti had previously been involved in interior work in San Lorenzo.
He is also said to have been employed by the late conservative populist Silvio Berlusconi, formerly Italy's prime minister, to carry out renovation work on a villa.
Meloni posted a photo of the angel on her Instagram page with the caption, "No, I certainly don't look like an angel," accompanied by a laughing emoji.
