The Home Office has wrongly denied compensation to numerous Windrush victims, a watchdog report has found, concluding that “further harm and injustice” has been caused as a result of systemic problems with the scheme.

More than £430,000 of extra compensation has been awarded to people affected by the scandal as a result of investigations by the parliamentary and health service ombudsman.

After handling 46 complaints about the compensation scheme, the ombudsman found that “justice has not been straightforward for many individuals and their families”, noting that the Home Office has sometimes made mistakes when handling claims, including wrongly telling people they were not eligible for compensation and failing to consider all the evidence provided.

The Windrush compensation scheme was set up in 2019 to offer compensation to people affected by the Home Office scandal which saw thousands of people miscategorised as illegal immigrants, many of whom were subsequently sacked from their jobs, evicted from their homes, denied NHS healthcare and in extreme cases detained and deported.

The scheme has been repeatedly criticised for processing delays, low offers and unfair rejections. More than 50 people have died after submitting a claim but before receiving any compensation.

Rebecca Hilsenrath, the parliamentary ombudsman, said she believed there were many more people struggling with their claims. “The Windrush compensation scheme was set up to right the wrongs of a scandal that inflicted harm on very many people. But our evidence shows that further harm and injustice are still being caused by failings in the way the scheme is working,” she said.

“Our report found people who had applied for compensation were being wrongly denied the money they were owed. We found recurrent reasons for this, suggesting these were not one-off issues but systemic problems.”

The report gives details of individuals whose compensation claims were initially denied but who later received substantial payouts as a result of the watchdog’s investigations.

The ombudsman believes that the conclusions from the “Spotlight on the Windrush Compensation Scheme” report could also provide useful lessons for public bodies attempting to offer compensation to people affected by the Post Office and the infected blood scandals.

“Those who have been failed cannot be let down all over again by the mechanisms established to provide compensation,” Hilsenrath said. “Given the number of people affected by the Windrush scandal, there may be many others who are unhappy with their experience with the Windrush compensation scheme. I encourage anyone who has a concern to bring their complaint to us.

A Home Office spokesperson said more than 2,600 people had been compensated so far, with £93.5m paid out. The new government has made a commitment to appoint a new Windrush commissioner and the home secretary is due to make an announcement soon about how cultural change can be “embedded permanently into the fabric of the Home Office”.

“This government is committed to putting right the appalling injustices caused by the Windrush scandal and making sure those affected receive the compensation they rightly deserve,” the spokesperson said.