The shocking incident occurred on New Year's Eve in a hostel in Dublin city centre.
The man was immediately provided with bed linen when he complained but the room he was allocated had no lock on the door which allowed other residents wander in and out of through the night.
In a statement, the Council said: "We were informed of this incident.
"The Dublin Regional Homeless Executive, (DRHE), has been assured by the accommodation provider that this is an isolated incident and was an inadvertent mistake. The man was assigned to a room which had not been cleaned prior to his arrival.
"They have apologised for the error.
"DRHE staff are in regular contact with service providers including on-site visits. We also proactively encourage anyone who uses emergency accommodation and wishes to make a complaint to do so.
"We have a designated a Complaints Officer who has circulated information posters and the Emergency Accommodation Guidelines for Service Users to all our accommodation facilities informing all users of our complaints process.
"The DRHE was on site in this premises in 2021."
Meanwhile a furious councillor has demanded that an Independent Regulator be appointed immediately to oversee all emergency accommodation in Ireland, after being sent photos and video footage of the Dublin incident.
Meath councillor Alan Lawes was a long time volunteer with Inner City Helping the Homeless, before it broke up, and has insisted that an outside body is urgently required to address the situation.
He told the Sunday World: "If you or I check into a hostel as a paying guest we’d go ballistic and leave if we were shown into a room that had blood stained bed sheets and pillow cases, we’d kick up a stink and rightly so and we certainly would be telling our friends not to stay there.
"Yet this is considered acceptable just because the person in question is homeless.
"Remember they are paying guests as well even if it is the state is covering the cost.
"I am not just singling this place out, I know of many many similar situations down here in Meath and all across the country."
He added: "I feel the Health Information and Quality Authority, (HIQA), should have their powers extended to allow them inspect emergency accommodation premises, or failing that a new regulatory body should be formed.
"I work in a hospital and I can tell you that the managers there s**t themselves when HIQA inspect the premises as any drop in standards can hit their funding.
"I feel the same stringent standards should be applied to owners of emergency accommodation.
"Another thing that has been brought to my attention is that owners of these premises instruct people they have to clean up after themselves and yet they don’t provide them with PPE equipment and as often as not the hand sanitisers are not working.
"The only reason the standards are so low is because owners know they will never be checked or if they are then it is a very rare event and that has to change."
Efforts to contact the hostel owners went unanswered.