The document, which was written by the former chairman of the charity David Hall, details four serious allegations of abuse that were made against Mr Flynn, who died in August.
Before his death, the former Dublin City Councillor was being investigated by gardaí in relation to two alleged sexual assaults.
The 12-page report written by Mr Hall, which was seen by Independent.ie, was sent to trustees and members of ICHH on Thursday evening.
It detailed events from July 30 of this year on how the charity dealt with the controversy.
The report outlined that the first two incidents occurred in May.
"One involved a 21-year-old male (classified by Gardaí as extremely vulnerable) in May 2021 being brought by taxi at 2.30am to the CEO’s home where [he] stayed the night,” the report says.
"This male was already housed and was not in need of accommodation. They claim they were drugged and awoke the following morning. [He ] presented to an adult emergency department the following day and was transferred to the sexual assault unit.
"The Gardaí believed the ICHH taxi account was used. 13 days later a person related to an ICHH Client was collected by taxi and brought to the CEO’s home.”
Another allegation was made 13 days later where “a party related to an ICHH Client was collected by taxi and brought to the CEO’s home. That night or the next morning an allegation was made to Gardai of sexual assault.”
Following the allegations of both assaults, gardaí seized Mr Flynn’s phone, searched his phone and took forensics from his home, the report states.
Gardaí also secured a court order seizing the taxi company records relating to the ICHH taxi account.
A third alleged sexual assault was reported to the charity on August 26.
"The alleged victim claimed [he] had been homeless and was accommodated by the CEO in accommodation provided by ICHH in Dublin,” the report says.
"While being accommodated by ICHH the CEO sent texts asking this person for sex. It was alleged the CEO transferred a specific amount of money via Revolut to this person to buy cocaine. The charity does not have a Revolut account.”
On September 5, a fourth person contacted the charity saying they were allegedly sexually assaulted by the former CEO and on September 9 made a statement to gardaí.
He met with Mr Hall and told him that after losing his job earlier in the year and facing eviction he turned to the CEO of ICHH for help.
The report continues: “[He] alleged [he] was sexually assaulted by the CEO and at the CEO’s home where a taxi had been sent to collect [him] (his address matched one of the addresses I had from the taxi account).
"[He] gave me details of alleged very serious sexual assaults and allegations of threats made against [him].
"[He ] showed me text messages from the CEO. [He] also alleged that [his ] phone has been taken by the CEO and should be in the CEO’s home.”
Mr Hall’s report will be discussed by members of the charity, including the board, in the coming days and Barrister Remy Farrell SC has been appointed to conduct a review into the controversy.
Attempts to reconstitute a new board of trustees for the charity failed earlier this week after Clare O’Connor, Gary Gannon TD and barrister Gavin Elliot withdrew their names.