"Around noon he was assaulted by an inmate," said Kelly Nantel, spokeswoman for the Massachusetts Department of Corrections. "The perpetrator has been identified and an investigation has been launched."
Geoghan, 68, was transferred to Suza Baranowski Prison, 100km northwest of Boston on 1 April. He still had some contact with other inmates despite being held in an individual cell for his own protection.
He was convicted in February 2002 for having sexually abused a 10-year-old boy in a swimming pool. He was also awaiting trial for a child rape that allegedly occurred in 1986, and is accused of having sexually abused more than 130 children.
The Roman Catholic Church, particularly the Boston Archdiocese, was rocked by the size of the scandal.
"Many of my clients would have rather seen Father Geoghan serve out his time in jail and endure the rigours of further criminal trials, so that his paedophile acts could have been exposed further"
Mitchell Garabedian, an attorney for many victims
The archdiocese itself came under further pressure for having sought to cover up Geoghan’s crimes by transferring him to six different parishes as accusations surfaced against him.
Geoghan's case eventually resulted in a multi-million dollar settlement with 86 of his alleged victims.
Mitchell Garabedian, an attorney for many of Geoghan's alleged victims told Reuters news agency that he was "surprised and shocked" by the former priest's death.
"Many of my clients would have rather seen Father Geoghan serve out his time in jail and endure the rigours of further criminal trials, so that his paedophile acts could have been exposed further," he said.
The Boston Archdiocese issued a statement saying it "offers prayers for the repose of John's soul and extends its prayers and consolation to his beloved sister Cathy at this time of personal loss."
A report recently released by the Massachusetts Attorney General's office said more than 1,000 children had been sexually abused by 237 Catholic priests over the past 60 years.