The pair aged 24 and 27 were held after the alleged assault four miles from where the floating accommodation block is moored.
Police received a complaint from an alleged victim at the Kika Beach Bar in Weymouth, Dorset in the early hours of Sunday, December 10.
The huge floating hotel housing asylum seekers in Portland Port to reduce the £8 million-a-day cost of hotels borne by UK taxpayers is a 15-minute drive from the alleged crime scene.
Staff at the bar confirmed to The Sun that police had been called to the premises and taken away hard drives containing CCTV footage.
But no one was seen being arrested inside the bustling night spot at the time of the alleged assault.
The unidentified migrant pair have since been released from custody and are on police bail while under investigation.
Hundreds of migrants have been moved to the Bibby Stockholm while their asylum claims are processed since it was opened in August.
They are free to roam in the area and many are taken by coach to Weymouth Town Centre – where many spend their £40.85 weekly spending money allowance.
The exact nature of the assault was not disclosed by police, but officers confirmed the alleged offence occurred inside the night spot.
Last week, more than 60 charities demanded the immediate closure of the vessel after an Albanian man died on board in a suspected suicide.
The dead man was named as Leonard Farruku, 27, who paid €4,000 (£3,436) to cross the Channel in a small boat last summer.
His sister Jola Dushku, 33, said the last time they spoke, Mr Farraku said the barge accommodation was acceptable but guards had treated detainees “like animals”.
News of the alleged sex attack will raise fears among locals concerned about the large migrant influx to their area.
One local source – who said he was aware of the sex claims – told The Sun: “Local people aren’t happy that the barge is closeby and have been fearing something like this might happen.”
A member of staff at Kika Beach told The Sun: “There was an accusation made last weekend, we have been spoken to by the police who have also looked through our CCTV.”
Dorset Police said: “We received a report at 3.10am on Sunday 10 December 2023 that a woman was sexually assaulted in Kika Beach on The Esplanade in Weymouth.
“Officers attended and two men, aged 24 and 27, from Portland were arrested on suspicion of sexual assault. They have been released on police bail while enquiries continue.
“An investigation is underway by detectives and we are continuing to support the victim as our enquiries continue.”