Video taken during the ceremony showed the priest failed to cover the boy's mouth and nose while he was being immersed into the water during baptism.
The baby died on the way to hospital and a postmortem found he had drowned, the baby's father Dumitru Gaidau told Romania's Publica TV.
He added: 'We all saw it, the priest didn't put his hand over the baby's mouth to stop water going in as he should have done and as they do at every other baptism.
'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.'
One of the boy's godmothers said. "The baby was crying as he went into 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.', she added.
Doctor Sergiu Raileanu, who examined the baby boy, confirmed the child died of drowning.
Father Valentin denied he caused the baby's death, saying he was experienced in baptism ceremony and knows what to do.
Police said they are investigating and charges will be made. If found guilty, Father Valentin will serve three years in jail.