A covert national security programme allows the FBI and US immigration authorities the power to indefinitely delay immigration benefits to Muslims and those from Muslim countries, according to an investigation by the American Civil Liberties Union.

The previously unknown programme, which began in 2008 under George W Bush to identify those with links to terrorism, has continued under President Obama to blacklist law-abiding applicants and profile Muslims as “national security concerns”, according to the ACLU.

Migrants who have travelled through or lived in areas of known terrorist activity, wired money back to their families, attended a mosque of interest to the FBI or even given a voluntary interview to the agency, can be labelled “national security concerns”, the report, published on Wednesday, says.

Jennie Pasquarella, the investigation’s author and an ACLU attorney, said the secret programme relies on “deeply flawed” mechanisms such as “over-broad watch-list systems” and religious, national origin and associational profiling.

“It not only catches far too many harmless applicants in its net, but it has overwhelmingly affected applicants who are Muslim or perceived to be Muslim”.

ACLU’s report said that the guidelines went beyond the criteria set up by Congress to determine eligibility for citizenship.

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