Democratic Republic of Congo state-owned mining company Gecamines insists it paid-in the money.
Gecamines presented accounts to auditors from the General Inspectorate of Finances (IGF) showing tax advances and loans to the Congolese state of more than $591 million, but only $178 million could be traced to the treasury's accounts, according to an IGF audit report seen by Reuters.
The report, which is dated May 31 but has not been publicly released, said the missing $413 million 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 $175 million paid to Gecamines as a signing bonus for a copper and cobalt project could not be traced to the treasury either.
Gecamines has long been dogged by accusations of corruption made by non-governmental organizations 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.
Since coming to office in 2019, President Felix Tshisekedi has overhauled Gecamines' leadership, replacing the executives most closely connected to previous corruption allegations.