Western and other donors have poured billions of dollars into Somalia, funding the army's battle against Islamist insurgents and helping to rebuild vital state institutions destroyed during decades of war between rival clan militias and Islamist warlords.
The donors complain President Hassan Sheikh Mohamud's cash-strapped government is not doing enough to tackle corruption and say the theft of scarce government resources has frustrated efforts to build a functioning state.
Nur Jumale Farah, Somalia's auditor general, said his office had investigated all 25 government ministries and would publish the findings when lawmakers return to the parliament next month following a recess.
The report will show "there are malpractices in the financial sector of most ministries", Farah told Reuters late on Friday, without elaborating.
The government did not respond to requests for comment.
Farah's task has been complicated by dissent within his 61-strong team. He said he had suspended seven members due to "bribe taking from ministries" they were investigating.
He linked the suspensions to a complaint lodged against him by several of the staff, who earlier this year wrote a letter to the prime minister complaining about Farah's working practices.
"The prime minister has given me his (vote of) confidence," Farah said in the Kenyan capital Nairobi.
Farah's report could further dent Somali government hopes for donors to start providing direct budget support, something they are reluctant to do due to graft concerns.
Western diplomats say the donors' relationship with Mohamud has never fully recovered from a 2013 corruption scandal involving the repatriation of overseas Somali state assets frozen at the outset of civil war in 1991. Mohamud and those close to him have repeatedly denied any wrongdoing.
Farah, who spent 17 years as an auditor in the United States, has been coming under increasing pressure to present the report after investigating the ministries throughout 2014.
Somalia's 2015 government budget stands at $216 million but is dwarfed by donor spending, seen at about $1 billion.
A 2013 report by U.N. investigators said individuals in Mohamud's government used the Somali central bank as a personal "slush fund", with an average 80 percent of withdrawals made for private purposes. The presidency and the then-central bank governor Abdusalam Omer have strongly denied that accusation.