According to the report by Sierra Leone's Auditor General looked at $19.5 million the government set aside for fighting the hemorrhagic fever from the start of the outbreak last May 2014 to October 31, 2014.
Most of the money came from tax revenues and donations by domestic institutions and individuals.
The report did not consider funds gain through U.N. agencies or international non-governmental organisations.
The fund was mostly spend on personal protective equipment, medical supplies, consumables and bonus payments to healthcare workers, the report said.
The report also stated that more than $3.3 million (Ghc11.2 million ) from the government's emergency health response account had no supporting documents to substantiate how they were spent.
A further $2.5 million (Ghc8.5 million) spent from the same account were missing receipts and invoices.
More than 10,000 Ebola cases have been reported in Sierra Leone since May, making it one of the hardest hit countries in West Africa with the worst recorded outbreak of the disease.
Bas on the World Health Organization figures the epidemic has been concentrated in West Africa and killed 9,253 people out of 22,999 known cases since December 2013.
However a statement from the Sierra Leone government said it had cleaned up a list thought to contain thousands of "ghostworkers" on its Ebola staff and would prosecute those who sought to swindle money from the government, tackling a problem that has dogged its fight against the epidemic.