About 5.8 billion yuan (USD 950 million) went towards "loan repayment, foreign investment, land requisition and house demolitions, office cash flow and other expenses not related to affordable-housing projects", the National Audit Office said on its website.
A total of 360 projects or organisations "embezzled" the funds, it said.
Housing costs which have spiralled in recent years despite government controls, have become a sensitive issue as ordinary Chinese find themselves struggling to afford a home.
But 110,000 families produced false documents to qualify for assistance unfairly, it added.
The state news agency Xinhua warned at the start of the year that tackling corruption in the affordable housing programme was "increasingly urgent".
"Many Chinese have become extremely sensitive to skyrocketing housing prices and any mishandling of housing resources," it said in an editorial.
House prices averaged 10,300 yuan per square metre in July, according to the independent China Index Academy, up 7.9 per cent year-on-year, an acceleration from 7.4 per cent in June.
Among the spate of scandals exposed in their anti-corruption campaign in recent months, several low-ranking officials have been reported to own multiple homes, sometimes in the dozens.
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