Police are investigating Father Valentin for accidential homicide after witnesses at the ceremony said the priest did not cover the baby's mouth during the ritual, The Sun newspaper reports.
Father Valentin had denied being responsible for the baby's death during the baptism in Moldova.
The six-week-old baby died on the way to hospital and an autopsy found he had drowned, the baby's dad Dumitru Gaidau told Romania's Publica TV.
Mr Gaidau, 36, said his son was clearly in distress during the ceremony.
"He couldn't inhale, his face turned blue and he was foaming at the mouth. He [the priest] said we should not interrupt this their ritual," he said.
"We couldn't believe it that he just put his hand over his belly and over the head and submerged him three times in the water."
Water was found in the baby's lungs.
The baby's godmother, Aliona Vacarciuc, said the baby had been crying as the priest submerged him in the water.
"We couldn't believe it but we thought the priest must know what he's doing, but he didn't. When we got him back there was nothing that could be done anymore," The Sun quoted her as saying.
When the baby's angry relatives confronted the priest, he told them he knew what he was doing and was experienced at baptisms, Ms Vacarciuc said.
If found guilty of accidental homicide, Father Valentin could spend three years in jail.