The priest was taken to hospital with serious facial injuries after the robbers beat him and smashed him over the head with a shovel, police in the town of Flieden near Fulda said on Wednesday.
They made off with several thousand euros in cash from the rectory safe. A 31-year-old chaplain who was also in the rectory suffered from shock.
It was not clear whether the cash belonged to the priest himself or was church money. The robbers broke directly into the priest's bedroom, woke him up and then assaulted him before taking the money from the safe.
They threatened the priest with a weapon and tied him up. The three men then put the money in a bag, assaulted the priest again, and fled.
“We are investigating all leads,” a police spokesman said when asked if it were possible the men had advance knowledge there was a large sum of money on the premises.
Police released no clues about the attackers, but said they were appealing to the public for information. The men wore dark clothing and black balaclavas.
The Fulda diocese in which Flieden lies was shocked by the attack. Bishop Heinz Josef Algermissen described the incident as a “malicious and brutal robbery.”
The priest had since returned home and “is doing well under the circumstances,” Algermissen said.