The home secretary is facing fresh pressure to scrap plans to house asylum seekers on barges after Legionella bacteria was discovered in the water supply of the Bibby Stockholm.

The Home Office removed all 39 migrants from the vessel in Dorset on Friday, in the latest embarrassing setback to a policy that has been beset with controversy and delay from the very start.

The removal came less than a week after the first migrants were transferred onto the barge – though legal challenges granted some a last-minute reprieve from having to board.

Care4Calais, which said it stopped 20 migrants from being moved onto the floating accommodation on Monday, said the discovery of bacteria shows their “concerns over the health and safety of the barge are justified” as they called on ministers to axe the policy.

Steve Smith, chief executive of the charity, said: “The Bibby Stockholm is a visual illustration of this government’s hostile environment against refugees, but it has also fast become a symbol for the shambolic incompetence which has broken Britain’s asylum system.

“The government should now realise warehousing refugees in this manner is completely untenable, and should focus on the real job at hand – processing the asylum claims swiftly, so refugees may become contributing members of our communities as they so strongly wish.”

Legionella bacteria, which is commonly found in water, can cause a serious type of lung infection known as Legionnaires’ disease.

None of those on the barge have shown signs of having the disease and are all being provided with a health assessment, the Home Office said.

It was not clear where the migrants would be moved to on Friday night.

Putting them in hotels would likely cause fresh embarrassment for the government, which procured the barge alongside other budget sites in an effort to reduce the £6m-a-day cost of housing asylum seekers in hotels.

The Home Office insisted disembarking those on board was a “precautionary measure” while further tests are carried out – but questions remain about who knew what and when.

Sky News understands routine testing of the water supply was initially carried out on Tuesday 25 July but the results did not come back until Monday 7 August – the same day asylum seekers began to board the Bibby Stockholm, which is docked in Portland Port.

However the Home Office was not made aware of the results until two days later on Wednesday 9 August. Six people boarded the vessel a day later but were later removed on the advice of the UK Health Security Agency, with a decision taken on Friday to remove everyone.

Labour’s shadow immigration minister Stephen Kinnock said it was “extraordinary” that it appeared proper checks had not taken place before migrants were moved on board.

“It’s absolutely right that the barge has to be evacuated but what a complete and utter shambles. This is a catalogue of catastrophe and government ministers should hang their heads in shame,” he told Sky News.

He said the government would not need to use “barges, hotels or military bases” if they tackled the backlog in the asylum system which has reached more than 173,000 – outstripping the 50,000 units he said were in the UK’s asylum estate.

He called the Bibby Stockholm “a floating symbol of Conservative incompetence”.

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Immigration minister Robert Jenrick was understood to be chairing meetings about the situation on Friday.

But one campaign group, No to the Barge, said Mr Jenrick should stand down from his government position with “immediate effect” after promising just days ago the Bibby Stockholm was safe.

On Wednesday, he told Sky News the barge was “perfectly decent accommodation”, despite earlier warnings from the Fire Brigades Union (FBU) that the vessel was a potential “death trap”.

The union reiterated its position in the wake of the latest development as they accused the government of ignoring their concerns.

Assistant general secretary Ben Selby said: “We wrote to Suella Braverman more than a week ago to demand a meeting to discuss these issues. We have had no response to that letter, and our fire safety and operational safety concerns remain.

“It remains our professional view that it’s a potential ‘death trap’ and an accident waiting to happen.

“However, Suella Braverman and her ministerial colleagues are hellbent on confining vulnerable people in jail like conditions on what is effectively a prison ship.”

It comes at the end of the government’s “small boats week” which was supposed to highlight new hardline policies for stopping Channel crossings.

The announcements were somewhat overshadowed by a row involving Tory deputy chairman Lee Anderson saying asylum seekers who don’t like barges should “f*** off back to France” and later admitting the government had “failed” to tackle illegal immigration.

Tory figures were largely silent on Friday night, though one unnamed senior figure was quoted in the i newspaper calling for Ms Braverman to go.

Scott Benton, a former Conservative MP who now sits as an independent, tweeted that the Bibby Stockholm had become a “complete and utter farce” – adding: “As if having porous borders isn’t bad enough, we can’t even move 39 illegal immigrants onto a barge properly.”

Mr Sunak has made “stopping the boats” one of his five key priorities in government.

However, he faced a further blow this week after 775 people were recorded crossing the English Channel on Thursday – the highest daily number so far this year.

It pushed the cumulative total of the number of people who made small boat journeys from France to the UK to more than 100,000 since 2018, when records began.