Detective Senior Sergeant Matt Russell of the Manningham crime investigation unit said the bodies were found by police who had been asked to conduct a welfare check.
He said the check was in response to a phone call from a relative living in the Ballarat/Daylesford region.
“One of the deceased was expected to be in the country region by last night and hadn’t returned,” he said.
He would not reveal whether any weapons had been found in the house or in which room the pair had been discovered
It is believed several firearms were found on the property where the man lived alone.
Police are seeking to ascertain when the man and woman died but believe the deaths could have occurred within the past 24 to 48 hours.
Bill Pantazis, who has lived across the street from the home for more than 40 years, said he knew the deceased man but not well. He thought the man had lived alone.
Mr Pantazis said the deaths came as a shock to him and his wife.
“It’s very quiet here, no trouble, no fighting, no nothing,” he said.
“When he came out I would say, ‘hello’. The other day he helped me put my trailer in the driveway.”
Mr Pantazis said he had not heard anything unusual before waking to the flashing lights of a police car parked on the street.
“We saw the police lights in the middle of the night, we thought maybe someone had tried to pinch something.”
Next-door neighbour Russell Wilson said he was surprised by the deaths.
“At 2 o’clock a couple of police officers knocked on my door and said there was an incident down the road and did I know of anything or any other problems in the area,” he said.
“It’s a very quiet street, we have never had any incidents here since u have been here and I have been here four years.”
Mr Wilson said it was a quiet neighbourhood where people tended to keep to themselves.
“I was shocked, something like this is most out of the ordinary.” Investigators will prepare a report for the coroner.