The Home Office is facing a new Windrush-style scandal after a landmark high court ruling found that the home secretary acted unlawfully by failing to provide documents to thousands of migrants proving they are in the UK legally.

The charity Ramfel brought the legal challenge along with Cecilia Adjei, a healthcare worker and mother of two boys aged 17 and 11, who came to Britain from Ghana in 2000.

The charity said hundreds of thousands of migrants were potentially affected by the Home Office’s failure to provide confirmation documents showing that people who apply to extend their visas are in the UK legally while the applications are being processed.

This is known as “3C leave”, an automatic form of immigration status while they wait for the Home Office to process their application.

Some have their jobs put at risk while others face difficulties accessing higher education, healthcare and the right to rent a home because they cannot prove they are here legally.

The case echoes the problems faced by the Windrush generation, who were unable to prove they were here legally and so struggled to work, rent and access benefits.

The judge in the case, Mr Justice Cavanagh, ruled on Friday: “The evidence clearly establishes that a substantial number of those on section 3C leave suffer real hardship through being unable to provide immediate documentary proof of their immigration status and attendant rights.”

He found that the failure to provide digital proof of status to those on 3C leave was unlawful. “The underlying purpose of the legislative framework is that there should be a hostile and unwelcoming environment for those who are unlawfully present and so who are undocumented. The corollary of this is that those who are lawfully here should not face the hostile environment. That can only happen if they are documented,” he said.

The judge urged the home secretary to take a “straightforward step” to avoid hardship for a substantial number of people.

Adjei welcomed the ruling. “What I went through while waiting for my visa to be extended by the Home Office was really stressful,” she said. “I was unable to prove that I had the right to work so was suspended from my employment as a healthcare support worker twice, without any notice.

“I have two children and have to budget very carefully, so we suffered real hardship when my wages suddenly stopped. I had to borrow money and visit a food bank just to get by. It was humiliating and scary as I didn’t have any way to prove to my employer that I still had the correct immigration status and the right to work.”

Nick Beales, the head of campaigning at Ramfel, said: “Time and again the government’s hostile environment traps and targets people with every right to be in the UK. They assured us they had learned from the Windrush scandal, but these words were clearly hollow. People on 3C leave have had their lives disrupted for years because they have been unable to prove their immigration status.”

Janet Farrell, a partner at Bhatt Murphy solicitors, which represented the claimants, said: “This is a significant victory for my clients and all those who through no fault of their own are left undocumented in an environment which demands proof of immigration status in order to access work, housing and healthcare or hold a driving licence or bank account.”

The Home Office has been approached for comment.