The grim discovery was made at Brookfield Lawn in The Lough after gardaí were called to the property on Tuesday afternoon.
It is feared the woman, who is in her late 50s, may have lain dead in the house for up to three years before she was discovered.
Her remains were found when local residents raised concerns about a pest control problem and a local company investigated.
Both Gardaí and Cork Fire Brigade attended the scene when human remains were found to be present in the property.
Paramedics also arrived on the scene.
The Office of the State Pathologist has been notified and the remains will be examined at the scene before being transferred to Cork University Hospital (CUH) mortuary.
A full post-mortem examination is expected to be carried out on Wednesday, possibly with the assistance of a forensic anthropologist.
Gardaí believe the woman involved is the resident of the house, although formal identification is likely to require examination of dental records and possibly even DNA.
It is clear that the woman lived alone in the property.
Local residents indicated that the woman had not been seen in the area for some time, possibly up to three years ago.
The woman kept to herself and some residents believed she had temporarily moved from the area after a death in the family.
The scene was sealed off by Gardaí to allow a full technical and forensic investigation.
However, there were no signs of forced entry into the property and there were no signs of any disturbances in the home.
Detectives will now examine the food items at the property, as well as bank, telephone and postal records, to try to determine the deceased's last known movements and activities.
Gardaí are carrying out door-to-door searches in the area to try to establish the last known public sighting of the woman.
It is the second death in Cork in recent times.
Last year, a Cork coroner returned an open verdict in the case of a man who lay dead and undiscovered in his home for 22 years – less than 100 meters from the main Cork-Limerick road.
The family of Timothy O'Sullivan, 61, who had been living in Britain, called for an urgent review of the dilapidated house rules as they warned no other family should have to go through what they went through.
The skeletal and partially mummified remains were found on January 13, 2023, by council workers inspecting an abandoned property on Beecher Street in Mallow.
Mr O'Sullivan, born in Caherciveen in Kerry but raised and worked in Britain, died sometime between January 9 and January 23, 2001, but was not discovered for 22 years.
The period before his death was determined by a dated Tesco store receipt, personal diary entries and the timing of his social security benefits.
Cork County Council officers had been to the property almost a decade earlier to board up broken windows and investigate a complaint from neighbors about a rodent infestation, but had not entered the Beecher Street house.
Mr O'Sullivan's Australian-based sister, Noreen Foster, had called to the Beecher Street property in July 2003, but was told by neighbors and gardaí that it was believed Mr O'Sullivan had moved to Great Britain some time earlier. Britain had returned.
In a statement read by lawyer Fiona O'Sullivan on behalf of Aidan Shine, a cousin of Mr O'Sullivan, and the entire O'Sullivan family, they called for an urgent review of Ireland's dilapidated housing rules.
This is intended to increase the powers of local councils to access abandoned homes, simplify the process of determining ownership and speed up the timeframe in which such properties are checked.
Mr O'Sullivan was born in Cahersiveen, Kerry, in 1939, but grew up in Britain, where he worked and married.
However, over the years he returned to Kerry regularly.
Around 1989 he moved back to Ireland and bought the property on Beecher Street.
His mother died in January 1990 and Mr O'Sullivan's wife, Barbara, later returned to her native Britain.
His sisters, Noreen and Maureen, were in regular contact with him through letters and Christmas cards, but did not hear from him until Christmas 2001.