The African women, who are from different orders in Sicily, reportedly got pregnant while on separate missions to their home country.
One of the nuns, a 34-year-old based at a convent in the northeastern town of Militello Rosmarino, in Messina, discovered she was pregnant after going to hospital with severe abdominal pains, the Gazzetta del Sud newspaper reports.
The second nun, a mother superior caring for the elderly in the southeastern city of Ispica, in Ragusa, has also discovered she is pregnant.
Salvatore Riotta, mayor of Militello Rosmarino, said he knew one of the nuns “well” and “regretted” the way the news had been leaked.
He told reporters: "There is regret for what happened. Our community of 1,200 inhabitants is baffled by the way some have treated the news, not as secretly as it should have been.”
The mayor added that the nun had taken her vows less than a year ago and was loved by everyone.
Sicily’s health councillor, Ruggero Razza, said he would launch an internal investigation to find out how the pregnancies became public knowledge.
He added in a Facebook post: “I wish to express my solidarity first of all to them and to their respective orders.
“I find it unfair that news that should have remained in the privacy of health facilities has become public knowledge.”
The women will be able to choose whether to leave the Order and raise their children, according to the Gazzetta del Sud.
The 34-year-old nun has been moved to a different order in Palermo, while the mother superior, thought to be about one month pregnant, returned home to Madagascar.
Pope Francis earlier this year admitted for the first time that the Catholic Church has an ongoing issue with priests and even bishops sexually abusing nuns. There is no information around whether the nuns were abused in this case.
Speaking to reporters aboard the papal plane in February as he returned to the Vatican from a visit to the United Arab Emirates, he said some of the nuns had been used as sex slaves and admitted more needed to be done to prevent it.
“It is true ... there have been priests and even bishops who have done this. I think it is still going on because something does not stop just because you have become aware of it,” he said, according to the Associated Press.
“We have been working on this for a long time. We have suspended some priests because of this.”