Gecamines holds minority stakes in several of the world's largest copper and cobalt projects, including Glencore's Kamoto Copper Company mine and China Molybdenum's Tenke Fungurume mine.
Gecamines has long been dogged by accusations of corruption made by non-governmental organisations and opposition politicians.
Gecamines has always denied all allegations of wrongdoing. Its secretary-general did not immediately respond to a request for comment on Saturday about the latest accusations.
Gecamines presented accounts to auditors from the General Inspectorate of Finances (IGF) showing tax advances and loans to the Congolese state of more than $591m, but only $178m could be traced to the treasury's accounts, according to an IGF audit report seen by Reuters.
The report, which is dated 31 May but has not been publicly released, said the missing $413m was presumed to have been misappropriated and that auditors would continue their investigations.
It did not specify when the advances and loans in question were made.
The report said another $175m paid to Gecamines as a signing bonus for a copper and cobalt project could not be traced to the treasury either, and faulted the company for failing to independently evaluate the levels of mineral reserves at its joint ventures with foreign investors.
Gecamines produced close to 500,000 tonnes of copper a year during its heyday in the 1980s, but it has since fallen heavily into debt and sold off its majority stakes in major mines.
The DRC is Africa's top producer of copper and the world's leading miner of cobalt, which is used in electric car batteries.
Since coming to office in 2019, President Felix Tshisekedi has overhauled Gecamines' leadership, replacing the executives most closely connected to previous corruption allegations.
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