A government watchdog has criticised the Home Office for failing to protect students wrongly accused of cheating in an English language test that they were required to sit as part of a visa application process.

About 2,500 students have been forcibly removed from the UK after being accused of cheating in the exam and a further 7,200 left the country after being warned that they faced detention and removal if they stayed. Many have protested their innocence; 12,500 appeals have been heard in UK courts, and so far 3,600 people have won their appeals.

The National Audit Office investigation into the Home Office response to reports of cheating in English language tests concluded that some people may have been wrongly accused and unfairly removed from the UK.

The organisation said it was still difficult to estimate accurately both the exact scale of cheating and how many innocent people may have been mistakenly accused because of the quality of evidence used to determine who cheated and the data kept by the Home Office on action taken against individuals.

Sir Amyas Morse, the head of the NAO, said: “When the Home Office acted vigorously to exclude individuals and shut down colleges involved in the English language test cheating scandal, we think they should have taken an equally vigorous approach to protecting those who did not cheat but who were still caught up in the process, however small a proportion they might be. This did not happen.”

In 2014 undercover filming by Panorama uncovered organised cheating in two of the 90 Home Office-approved centres offering the exam required for visa extensions. The government responded by asking the test provider, the US-based Educational Testing Service (ETS), to assess whether the 58,459 tests taken between 2011 and 2014 were valid. The US company made checks and concluded that virtually every test taken was suspicious.

The Home Office suspended the licences of some test centres and revoked the visas of those accused of cheating. ETS had identified 97% of all UK tests as “suspicious”; it classified 58% of as “invalid” and 39% as “questionable”.

Campaigners have questioned whether it is plausible that 97% of people taking the test of English for international communication (Toeic) could have been involved in cheating. The NAO was unimpressed by the Home Office’s scrutiny of the ETS investigation into its own test results and highlighted several shortcomings in the official response.

“The Home Office did not have the expertise to validate the results,” the report said. “We could find no evidence that the department had actively looked at whether innocent people were wrongly assessed as cheats … We saw no evidence that the department considered whether ETS had misclassified individuals or looked for anomalies.”

The report noted that Home Office staff were not equipped to scrutinise ETS’s analysis of test voice recordings, and its conclusion that virtually all tests were suspicious should be classified as invalid. “In 2014, a delegation of five civil servants visited the US to understand the process that ETS used and to listen to a small number of recordings. None of the people in the delegation had expertise in the technology or techniques used. Instead, they relied on assurances from ETS that the voice recognition technology was suitable for the task,” the report stated.

NAO researchers found a number of errors in the ETS files, highlighting that the company had wrongly categorised 6,000 people taking the test as British nationals. Apart from basic checks, “the department did not carry out any independent checking or testing of the data, trusting that ETS had correctly categorised individuals as having invalid or questionable results,” the study added.

Bindmans, the legal firm that has represented dozens of Toeic students, told the NAO that ETS had failed to provide information and documents to which the individuals were entitled in order to challenge the allegation of cheating.

The report found that thousands of people suspected of cheating had low scores in multiple-choice tests, indicating that they were not being given the correct answers by an invigilator (as footage from Panorama had shown happening in one test centre).

A Home Office spokesperson said the student visa system “was subject to widespread abuse in 2014”. “The report is clear on the scale and organised nature of the abuse, which is demonstrated by the fact that 25 people who facilitated this fraud have received criminal convictions.”

Nazek Ramadan, Director of Migrant Voice, said: “The report clearly proves what we have long suspected – that the Home Office, led by Theresa May, failed to scrutinise the evidence given to them by the testing company and shockingly chose to accept it at face value, despite multiple significant flaws in the data.

“The way the Home Office has treated these students makes a mockery of the British justice system. And the impact has been devastating. Those still living under the shadow of the allegation and fighting to clear their names live every day in growing despair. Stripped of their rights, many are destitute and suffering severe mental health problems. Many have contemplated or attempted suicide.

“All those accused must be given the chance to sit a new, secure English test and, if they pass, have their names cleared and their visas given back to them, with enough time to complete their studies.”

The Labour MP Stephen Timms said: “Thousands have been unfairly penalised, with catastrophic consequences for many. The home secretary has promised an oral statement to Parliament about this scandal. He must now give those affected, who remain in the UK, a chance to clear their names – for example, by offering them a fresh English test.”