This comes as the world's fastest-growing Ebola outbreak on record continues to outpace efforts, and the virus has spread into eight provinces in Congo and into neighbouring countries, Kenya and Uganda.
The revelations renew long-standing questions about transparency and accountability in Congo, a country battered by decades of major epidemics, including repeated Ebola outbreaks.
In recent months, The Associated Press reported extensively on strikes of frontline health care and support workers over unpaid salaries, bonuses and dangerous conditions in eastern Congo.
Previous Ebola outbreaks were marked by allegations of corruption and mismanagement of funds, which experts said have contributed to the mistrust of local communities, complicating the efforts to halt the spread.
"Many of those involved in the response - who sometimes risk their own lives to save others - say that they have not been paid," Prince Bahati, a nurse from Bunia, a town in eastern Congo which is at the centre of the outbreak, told the AP.
Dr Jean Kaseya, director general of the Africa Centres for Disease Control and Prevention, told reporters last week that since the beginning of the epidemic, $US962 million ($A1.4 billion) from international donors has been disbursed to organisations working on Ebola response in eastern Congo.
But only $US200 million ($A286 million) has been accounted for by organisations working on the ground, which include UN agencies such as the World Health Organisation, UNICEF, the World Food Program, and international charities like Save The Children and Medecins du Monde, as well as local aid groups.
Only one-third of the organisations attended a recent meeting organised by Congo's health ministry and provided their financial records, Kaseya said.
Those attending organisations said they received $US228 million ($A327 million), of which $US127 ($A182) million had been spent and around $US100 million ($A143 million) remained available.
"This represents a significant lack of transparency," the Africa CDC said in a statement.
"It is unacceptable for organisations to receive hundreds of millions of dollars to intervene in a country facing a major health emergency without providing a transparent account to the national authorities responsible for co-ordinating the response."
Kaseya said the agency would work closely with the Congolese authorities to investigate what had happened with the remaining money.
The Ebola outbreak in Congo has reached an eighth province in the country's north, authorities said on Sunday as the spread of the world's fastest-growing outbreak of the disease on record continues to outpace response efforts.
Authorities have recorded at least 9,400 cases, including over 4,500 deaths, in the outbreak declared in mid-May, making it the deadliest in Congo's history.
