The Home Office has been accused of inflicting irreversible damage on the life of a pharmaceutical expert by misusing a controversial clause in immigration law to try to force her out of the UK.

Nisha Mohite finally received indefinite leave to remain (ILR) this week after a government review found she was one of more than 300 highly skilled migrants who the Home Office had wrongly tried to force to leave under paragraph 322(5) of the immigration rules.

The paragraph is a discretionary, terrorism-related clause that the Home Office’s internal guidance states should only be used when the applicant’s misconduct is on a par with “criminality, a threat to national security, war crimes or travel bans”. However, the Guardian has reported extensively on the Home Office’s use of the clause to try to force applicants – including teachers, doctors, lawyers and engineers – out of the UK for making minor and legal amendments to their taxes.

Appealing against a decision can take years, during which time the applicant cannot work or rent property, and neither they nor their immediate family can use the NHS. Many feel forced to appeal because accepting the decision makes it highly unlikely they will ever get a visa for any other country.

Since the Home Office used the clause to reject Mohite’s application for indefinite leave to remain (ILR) in 2016 because of a tax amendment, she has lost her job and her home. Mohite, who specialises in the development of anti-cancer and anti-psychotic drugs, sold her possessions, spent all her savings on legal fees and is now heavily in debt.

On receiving her ILR, Mohite said: “While I’m delighted my two-and-a-half year torture is finally at an end, I’m furious and frustrated that the Home Office insisted on fighting through court after court, wrecking my life despite me proving repeatedly this was all an honest mistake. The damage they have done to me is irreversible.”

In November, the government released the findings of its review into the Home Office’s use of the controversial power in cases between January 2015 and May 2018.

Apart from the 300 people found to have had the paragraph wrongly used against them, the review suggested that up to 87 highly skilled migrants had already been wrongly forced to leave the UK. They were mostly people who had lived in the UK for a decade or more and had British-born children. Many were given just 14 days to leave and were no longer eligible for a visa to visit the UK or any other country.

The review found that another 400 people may have been wrongly affected. However, the total number is likely to be substantially higher with hundreds of cases still to be heard; the first-tier tribunal has 372 outstanding appeals against paragraph 322(5) and another 242 cases that could be allowed.

Mohite’s accountant made a mistake in her 2010-11 tax return, resulting in her self-assessment tax return showing an incorrect income, even though she had paid all the tax she owed. A new accountant discovered the error in 2013 and Mohite immediately paid the money owed.

But when Mohite applied for ILR, the Home Office said the amendment was evidence of dishonesty and rejected her application.

The notes taken by the caseworker who interviewed Mohite said her evidence was found to be “genuine”. However, her refusal letter stated: “Paragraph 322(5) is a suitable rule which may be used in a wide range of cases. Your caseworker has correctly identified undesirable conduct.”

Mohite’s case was one of just 56 which the Home Office identified as requiring a formal reconsideration.

A Home Office spokesperson said: “Miss Mohite was granted indefinite leave to remain after her case was reviewed.”