A senior official at Uganda's finance ministry confirmed that accounts in the country's central bank had been hacked but he downplayed the extent of the losses.

The Bank of Uganda had said late on Thursday it was awaiting a police investigation into a news report that offshore hackers stole 62-billion Ugandan shillings ($16.8-million) from the central bank.

State-owned New Vision newspaper reported on Thursday that hackers, identifying themselves as "Waste", accessed the Bank of Uganda's IT systems and illicitly transferred the funds earlier this month.

State minister for finance Henry Musasizi confirmed the hack and said the police's Criminal Investigations Department and the Auditor General were probing the incident.

"It is true our accounts were hacked into but not to the extent of what is being reported. When this happened, we instituted an audit and at the same time, and investigation," he told parliament on Thursday.

"To avoid misrepresentation of facts, I wish to indulge the House that we be patient that when the audit is finalised, which is now at the tail-end, I come and report."

The hacking group, based in Southeast Asia, sent part of the stolen money to Japan, New Vision said, citing unnamed sources at the bank.

New Vision said the central bank had successfully recovered over half of the money from the hackers.

Uganda's biggest independent newspaper, Daily Monitor, reported that the theft may have involved collusion by insiders.

Cyber thefts from banks and other financial service providers, including telecom firms, have occurred many times in Uganda. However, police officials have said that some banks are hesitant to publicly acknowledge such incidents due to fears of alienating customers.