British MPs have called on the government to suspend “secretive” multimillion pound funding programmes to the oil-rich Gulf that they allege could place the UK at risk of complicity in human rights abuses in Saudi Arabia and Bahrain.

The all-party parliamentary group on democracy and human rights in the Gulf said in a report that programmes supported by the Integrated Activity Fund (IAF) had been run with “absolute minimum levels of accountability, transparency and due diligence in spite of being repeatedly implicated in human rights violations”.

The report added that IAF-backed institutions in Saudi Arabia and Bahrain “have whitewashed human rights abuses, placing the UK government at risk of complicity in abuses themselves”.

The report, due to be published on Tuesday, said the IAF had spent £53m between 2016/17 and 2019/20.

Both Saudi Arabia and Bahrain are considered important UK partners in the Middle East, with the latter hosting British and American naval bases. But both are autocratic states that have poor human rights records.

In Saudi Arabia, Crown Prince Mohammed bin Salman, the kingdom’s day-to-day leader, has been accused of overseeing an increasingly oppressive state as scores of activists, businessmen, royals, bloggers and academics have been detained.

US intelligence agencies concluded that he must have authorised the operation that led to the 2018 murder of Jamal Khashoggi, the veteran journalists killed by Saudi agents in the kingdom’s consulate in Istanbul. Riyadh blamed Khashoggi’s murder on a rogue operation and Prince Mohammed denied any involvement.

Activists accuse Bahrain’s ruling royal family of a years-long crackdown targeting members of the minority Shia community since the authorities crushed a popular uprising during the 2011 Arab Spring.

There are about 1,500 political prisoners in the small kingdom, while almost 300 Bahrainis have been stripped of their citizenship, according to the Bahrain Institute for Rights and Democracy, which produced the all-party report.

Bahrain says it has been countering Shia militants it accuses of carrying out attacks and seeking to destabilise the nation.

The IAF was launched in 2016 and began funding programmes in the Gulf the following year, under the oversight of the Cabinet Office. It was replaced by the Gulf Strategy Fund (GSF) in 2020, which falls under the Foreign Office.

The report, endorsed by 10 of the group’s 17 members, including Sir Peter Bottomley, the veteran Conservative, accused the government of being “misleading” and “deceptive” about the IAF, saying it claimed it was a fund for health, sport and culture and was not used for security matters in Bahrain.

The Foreign Office said all co-operation through the GSF was “subject to rigorous risk assessments to ensure all work meets our human rights obligations and our values”.

“We do not shy away from raising legitimate human rights concerns, and encourage other states to respect international law,” it said.

But the report said: “As parliamentarians, we have seldom encountered so much government resistance as when we began investigating the source of this funding; the secretive Integrated Activity Fund (IAF) and the Gulf Strategy Fund (GSF).”

According to the government, the GSF supports Prince Mohammed’s Vision 2030 reform plan in Saudi Arabia; while in Bahrain it backs reforms to “deliver long-term security and stability”. Meanwhile, in the United Arab Emirates it “secures increased commitment” from Abu Dhabi to work with the UK to identify and respond to threats such as illicit finance, cyber crime and terrorism.

It also supports programmes in Kuwait, Oman and Qatar, including helping preparations for Doha’s hosting of the 2022 football World Cup.

But the all-party report said the IAF and GSF fund programmes to “bodies in Bahrain and Saudi Arabia that continue to be implicated in serious human rights and international law violations”.

“Government funding to GCC states through the GSF should be immediately suspended pending an independent inquiry into its implication in human rights and international law violations,” it said.