The disturbing find, shortly after 1pm yesterday, was made as gardaí were processing 90 calls in relation to the case.
These calls to the garda incident room at Midleton Golf Club followed Tuesday's televised reconstruction of the schoolboy's disappearance on January 4.
On that day, Robert left his house on his new BMX bike, a Christmas present from his parents.
At 2.36pm that day he made a phone call to a friend living close by before his credit ran out. His mobile phone was turned off shortly afterwards.
That evening, at 5.30pm, Robert's bike was discovered against a ditch, near the local golf club, half a mile from his home.
His parents, Mark and Majella, puzzled by the fact that his phone was disabled, started looking for him.
At 10pm gardaí were alerted.
The intensive search began on January 5, sometimes involving more than 1,000 people civilian volunteers, gardaí, army and civil defence.
This week, a child resembling Robert cycled his bicycle from the family home at Ballyedmond, in a reconstruction of the boy's last known movements.
After that, gardaí said they wanted to talk to a man reported to have been seen in a field near the boy's house. The dark-haired man was described as being smartly dressed at the time.
The man was seen in Egan's Field on the day Robert was last seen and was spotted again at 2.40 pm in the same place.
Gardaí were also hoping to interview three men who were playing golf at the East Cork Golf Club on Tuesday January 4 the day Robert went missing. These men have made no attempt to contact gardai despite repeated requests.
Further information was also being sought on a man seen driving a small red van in a car park near Curragh Woods on January 4.
The unsettling turning point in the operation came shortly after 1pm yesterday. Volunteers, who were focusing on rural scrub land near Whitegate, spotted a limb, said to be that of a young person, protruding from the undergrowth.
The garda incident room in Midleton received the report at 2.15pm and officers were immediately dispatched to the scene.
Superintendent Kevin Donohoe of the Garda Press Office, said the body had been discovered following a search by gardai, army personnel and volunteers.
"We have an area at Inch beach cordoned off and we are now commencing a technical examination. It's lying in an inaccessible area so at this stage I can't confirm either age or gender," he said.
A local priest accompanied the gardaí and prayers were said at the scene which has been cordoned off.
Members of the Dublin-based Garda Technical Bureau will this morning examine the area hoping to produce vital clues to the circumstances of Robert's disappearance.
The body was found in scrub land, adjacent to a boreen off the main access road to Inch Strand.
Later, back at the incident room, those who were searching at Inch strand, many of them civilian volunteers, were visibly shocked and distressed.
Some searchers were friends of the Holohan family or had children attending the same school as Robert.
A second body discovered yesterday in Midleton was understood to be that of an elderly man.
His body was found in the town, beside the Owenacurra river, near the Cork Road bridge last evening. Gardaí did not believe the discovery was related to the Holohan case.