The 63-year-old has been nominated by Micronesian nations to be the next Pacific Islands Forum (PIF) secretary general.
PIF nations agreed to his appointment, to take effect next year, at a special leaders retreat a fortnight ago attended by Foreign Minister Penny Wong.
However, since the nomination of Mr Waqa, Nauru's leader from 2013 to 2019, serious concerns over his candidacy have been raised.
An Australian Federal Police investigation, as reported by the ABC, alleges Mr Waqa and other Nauru officials received kickbacks from Australian company Getax as it lobbied for access to Nauru's phosphate reserves.
An AFP spokeswoman said Getax had been charged with bribing a foreign public official in 2020, but as the matter remained before the Brisbane District Court, it would not make further comment.
In 2014, Mr Waqa's government sacked Nauru's chief magistrate and suspended the chief justice, disrupting the rule of law in the island nation.
Mr Waqa's time in office overlaps with Australia's use of an offshore detention centre in Nauru, which was used to house hundreds of asylum seekers, including women and children.
In 2018, Mr Waqa accused self-harming children at the centre of "working the system ... just to get to Australia" and banned Doctors Without Borders (MSF) from treating patients on the island.
MSF then published a report on clients in the centre titled 'Indefinite Despair', saying half of its patients required treatment for psychosis and a third had attempted suicide.
Mr Waqa's government also introduced a severe clampdown on media freedom, banning Facebook, denying journalists entry and detaining a Kiwi journalist after she interviewed a refugee at a previous PIF summit.
Despite his leadership record, Senator Wong told AAP Australia would abide by his PIF appointment as it was part of an "agreement that allowed the family to reunite".
Micronesian nations - Nauru, Kiribati, the Federated States of Micronesia, Marshall Islands and Palau - were afforded the opportunity to nominate PIF's next leader as part of a pact to restore Pacific unity; the Suva Agreement.
Leaders from PIF's 18 members rubber-stamped his candidacy at the Nadi retreat.
As PIF operates on a consensus model, that included Australia and New Zealand.
"Australia is committed to uphold the Suva Agreement which forms the basis for strengthening the Pacific Islands Forum going forward," Senator Wong said.
"Under the Agreement, the position is rotated, and Micronesian members of the PIF worked to nominate the next Secretary General. All Pacific leaders agreed to the nomination."
Australia has poured in millions of dollars and months of diplomacy - with Senator Wong making trips to 16 different Pacific nations since coming to office in June last year - to patch up PIF.
PIF's position as the Pacific's premier regional body was threatened last year when Kiribati withdrew, only for it to return this year after pleas from Australia and the new Fiji government, led by Sitiveni Rabuka.
Senator Wong said a united PIF was "central to ensuring we live in a region that is peaceful, prosperous and resilient".
"The Suva Agreement was key to securing unity, and will help strengthen the PIF," she said.
Australia and New Zealand have agreed to pay for PIF's operations through to 2026 as part of the Suva Agreement, which will cost Australia around $A2.3 million.
