During a service Sunday at the Apostolic Palace, two children released the doves as a sign of peace while standing next to the pope after a prayer and a call for an end to violence in Ukraine.
Immediately after the doves were released, a seagull swooped in and began to attack both birds. Not long after, a black crow also began pecking at the doves.
It wasn't clear whether the doves survived the attacks.
Animal welfare group Ente Nazionale Protezione Animali called on Francis to stop the practice of releasing the doves.
"Do not use more animals and sacrifice their lives to outmoded traditions," the group said in a statement.
The group said the doves are born in captivity and don't have the ability to fight off predators, the Italian news agency ANSA reported.
"They cannot even use camouflage: their white color (is) very eye-catching in nature," the statement said.