Sir John Bourn, the head of the National Audit Office (NAO), has told the UN that he cannot continue working with the WHO and its controversial Japanese director-general, Dr Hiroshi Nakajima.
The British move is thought to be unprecedented and is likely to cause uproar at the proceedings of the World Health Assembly, WHO's governing body, at present under way in Geneva. Donor countries are already highly dissatisfied with Dr Nakajima's leadership and demanding reform.
Dr Nakajima is understood to be considering applying for a third term as head of WHO, despite the widespread discontent and a scandal over allegations of influence-peddling that surrounded his re-election two years ago.
The NAO, an independent body responsible to Parliament, has been the external auditor to WHO since 1978. Its report into the allegations over Dr Nakajima's election campaign concluded that there had been improper letting of WHO contracts to members of the board that voted for his renomination.
The director-general's attitude to the Africa report seems to have been the last straw.
"A high degree of co-operation and trust between an organisation and its external auditor are essential if the external audit function is to operate efficiently," Sir John wrote in a letter to the World Health Assembly dated 24 April. "In view of the attitude of the Secretariat I have, with regret, concluded that these essential requirements no longer obtain."
The NAO would complete its commitment to audit the WHO for the next 11 months but would not apply again for the contract, Sir John said.
According to the Africa report, auditors found a shocking lack of financial controls, fraudulent claims for education grants, irregular procedures for appointing staff and cases where staff had not repaid substantial cash advances to WHO.