Hundreds of protesters have blocked an attempt to collect asylum seekers from a London hotel and take them to the Bibby Stockholm barge.

Arrests were made as police waded into the crowd blocking the road near a Best Western hotel in Peckham. It was not until 3pm, seven hours after it turned up, that the coach sent for the asylum seekers was able to leave the area – without asylum seekers onboard – and a number of police vans carrying protesters who had been detained were also able to leave.

Deputy assistant commissioner Ade Adelekan of the Metropolitan police said: “A total of 45 people have been arrested and taken into police custody for offences including obstruction of the highway, obstructing police and assault on police.”

The home secretary, James Cleverly, condemned the protesters and said they “will not … deter us from doing what is right for the British public”. But the scenes illustrated the challenges the government may yet face when it comes to carrying out deportations to Rwanda.

It emerged on Thursday that the Home Office was abandoning plans to move asylum seekers in Margate to the Bibby Stockholm in the wake of protests there.

Meanwhile, Humza Yousaf, Scotland’s outgoing first minister, denounced the Home Office’s “inhumane” and “cruel” detention raids on asylum seekers and urged the UK government to scrap the policy.

At least eight asylum seekers living at the Best Western were told a week ago that they would be collected on Thursday morning and relocated to the Bibby Stockholm, moored at Portland in Dorset. The coach was expected to collect other passengers along the way, but it was blocked in when it was surrounded by protesters after pulling in at a bus stop at about 8am.

At least one person received medical attention when they were knocked to the ground after police moved in at about 12.30pm.

The people due to be removed were said to include teenagers attending colleges in the area. A number of men staying at the hotel said they feared the conditions that would await them on the Bibby Stockholm, where an Albanian man named Leonard Farruku died last year in a suspected suicide.

One said: “We are also concerned this is happening at the same time as the government’s Rwanda plans have gone through. But it’s encouraging to see this sort of support.”

Adelekan said officers engaged with protesters at the scene and warned them they could be arrested.

In Edinburgh, Yousaf told MSPs during first minister’s questions: “I deplore the inhumane Home Office enforcement action that we have seen. Detaining people to forcibly remove them to Rwanda is cruel, and punishes some of the most vulnerable in our society.”

Yousaf was asked by the SNP MSP Karen Adams about the Guardian’s report on Sunday that the Home Office was to start detaining asylum seekers for forced deportation to Rwanda.

He said: “At times like this, we all have an obligation to just step back. Actually think about what’s going on here, in a country, the UK, where those who flee persecution, war or extreme poverty, come to our shores.”

Figures released on Thursday undermined Rishi Sunak’s claims that his Rwanda plan was working by putting off asylum seekers from trying to reach the UK. They showed that 711 people arrived by boat on Wednesday, more than half of the number who crossed during the whole of May last year, and a record for a single day since September.

One of the coordinators of the protest in Peckham, Kojo Kyerewaa, of Black Lives Matter, said: “Our friends who are at a Home Office hotel got notification that they were going to be taken to the Bibby Stockholm today.”

He said they were given a week’s notice and that “because of the bonds and relationships they’ve got in the community, we were made aware of that and organised a discreet action … so that they would not be abducted and taken away”.

Kyerewaa said the protest was inspired by a similar one in Margate last week, where a coach was prevented from taking 22 asylum seekers to the barge.

“We know that the residents don’t want to leave and we know that the Bibby Stockholm is a dangerous place to put anyone. It’s unsanitary and one person has taken their own life being there and there’s been multiple attempts of suicide by people told that they’re going to the Bibby Stockholm,” he said.

The action is believed to be the first of its kind in London since 2022, when protesters gathered for hours to block a van transporting a man arrested for immigration offences.

Some of those organising the action were from Black Lives Matter and the Southwark and Lambeth Anti-Raids network, while others were understood to be friends in the community, including those who taught the asylum seekers English at college.

A Home Office spokesperson said: “This behaviour is intimidatory and aggressive. As part of our commitment to significantly reducing the use of hotels, asylum seekers are being moved into alternative accommodation to reduce costs on the taxpayer.

“We have returned 150 hotels to local communities and we work closely with accommodation providers to manage the exit process in a way which limits the impact on local authorities and asylum seekers.”