The body was recovered from an open pit on a farm in Rahaniskey, near Whitechurch, on the northern outskirts of Cork City after a painstaking two-hour operation conducted under lights last night.
The remains were taken to Cork University Hospital were an autopsy will take place this morning.
Supt Con Cadogan said gardaí are keeping an open mind on the case pending official identification of the remains and the outcome of the postmortem.
However, he confirmed that the pit is close to where missing father of two Diarmuid Twomey, 31, was last seen in the early hours of December 20.
His mobile phone was found on the neighbouring farm, about 90m away, at about 11am that day.
He also said a garda family liaison officer briefed Mr Twomey’s partner, Ciara Byrne, on the developments last night.
Gardai were alerted around 4.30pm yesterday as contractors were drawing slurry from the 18m by 12m, 3m-deep slurry pit located on a farm in the Whitechurch area.
The slurry level had dropped about 60cm when they made the grim discovery.
Although the open pit is surrounded by a 1.5m wall, topped with fencing, it is easily accessed via two gates.
Garda cordoned off the area and after an initial risk assessment, they called in members of Cork City Fire Brigade.
Working under lights, and wearing breathing apparatus and biohazard suits, they spent two hours retrieving the body.
Mr Twomey went missing in the early hours of Sunday, December 20, after attending his nephew’s 18th birthday in Bishopstown the night before.
He and Ms Byrne went to a relative’s house in Fairhill afterwards before she caught a taxi home to Carrignavar at around 3am.
Mr Twomey said he felt unwell and told her he would follow along later.
He was seen by a taxi driver walking on the main Cork to Whitechurch road, close to Whitechurch village, at around 4.20am. It i believed there was another sighting of him walking back towards Cork an hour later.
Despite extensive searches involving gardaí, coast guard air and ground units, missing persons associations, and dozens of local volunteers, and several garda appeals for information, there has been no trace of Mr Twomey since.