Britain’s biggest Catholic aid charity, Cafod, has been suspended from an international scheme which aims to protect aid beneficiaries from sexual exploitation and abuse.

The £50m-a-year charity has failed an audit by the Humanitarian Quality Assurance Initiative (HQAI), which vets how charities meet core humanitarian standards, including how complaints against aid workers are handled. It scored zero out of a possible five points for its handling of complaints.

The charity has confirmed that it sacked a staff member in Ethiopia after allegations of sexual misconduct with a juvenile boy. Earlier this year, it was forced to sack another aid worker implicated in the Oxfam sexual abuse scandal after the 2010 earthquake in Haiti.

Cafod’s suspension from the HQAI emerged before a government conference on tackling exploitation and harassment in the aid sector in the wake of the Oxfam scandal. The conference on Thursday will be led by the international development secretary, Penny Mordaunt, and the aid sector is expected to commit to “overcome the power imbalances and structural inequalities that give rise to sexual exploitation, abuse, harassment and bullying”, according to the summit’s draft commitments.

Checks on Cafod programmes in Ethiopia and Kenya by the Geneva-based HQAI uncovered “serious and connected weaknesses around complaints programmes”. Cafod works with more than 300 partner organisations around the world and the auditors reported: “Cafod does not work systematically with partners to ensure communities are made aware of the expected behaviour of humanitarian staff regarding the prevention of sexual exploitation and abuse.”

Cafod’s vision is of “a world transformed to reflect the kingdom of God”. It received £9.4m in government grants – mostly from the Department for International Development, the European Union and the United Nations – in the past year and £33m from supporters, mostly Catholic worshippers. It said it was working to tackle the problems, including installing new software systems and rolling out staff training.

There is rising concern at the Charity Commission about a lack of reporting of serious incidents by charities. Serious incident reports that centred on safeguarding concerns, including exploitation and abuse of aid beneficiaries and child protection cases, reached 464 in August as part of a sharp rise in the number of reported serious incidents this year. However, most of the reports have only been made by a tiny minority of registered charities.

Problems with safeguarding disproportionately affects overseas aid and famine relief charities. Almost a third of the 1,228 safeguarding reports submitted to the charity commission between February and May related to such organisations, even though they only account for 7% of all charities.

According to HQAI, people receiving Cafod’s help in its HIV and Aids programmes in Ethiopia and food security programmes in Kenya did not know what behaviour was acceptable by its aid workers and recipients did not have “access to safe and responsive mechanisms to handle complaints”. It listed seven breaches of the internationally recognised core humanitarian standard and scored the charity zero out of five for ensuring complaints are “welcomed and addressed”.

Cafod is the first charity to be suspended under the initiative, despite helping fund the development of the core humanitarian standard which the audit checks.

After the Oxfam scandal, Cafod insisted it had systems in place to prevent “all forms of abuse and misconduct”. Chris Bain, the director, signed an open letter in February calling on charities to “create an environment where people feel safe, and confident to report any behaviour that makes them feel uncomfortable or which threatens them or their communities”.

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Bain insisted in a statement on the charity’s website: “We have robust safeguarding and whistleblowing policies and practices in place which are regularly reviewed, to ensure that vulnerable people are protected.”

The HQAI has given Cafod six months to carry out “major corrective action” to address “systemic weakness”.

Geoff O’Donoghue, Cafod’s operations director, said: “We have some failures in this, but to say that we failed completely is wrong. If there were profound problems, they would have withdrawn the certificate and not suspended it. We accept the challenge that our complaints handling is not strong enough, is not good enough.”

He conceded there was a risk that abuse cases may not have been reported, but insisted there were good complaints systems in some places where the charity operated.

In Cafod’s latest annual report, Bain said: “We are currently in discussion with the core humanitarian standards overseeing body with a view to improving the way that we manage feedback and complaints. We are also running refresher training on safeguarding and our code of behaviour for every member of staff and developing improved training programmes for our international staff working on these issues with local partner organisations around the world.”