The pair were charged with one count each of abuse of office following the sanctioning of charges by the Public Prosecutions director (DPP) Christopher Pryde earlier on Thursday.
The two are alleged to have interfered in an active investigation into a financial mismanagement case involving former staff of the University of the South Pacific almost four years ago reports RNZ Pacific.
Acting Police Commissioner (ACP) Sakeo Raikaci said they were kept in custody at the Totogo Police Station and will be taken to the Suva Magistrates Court at 8am local time.
"Bainimarama and Qiliho were brought in for further questioning today [Thursday]. Upon the completion of the questioning via video recording interview, the two were formally charged," ACP Raikaci said.
"As advised by Pryde, the special task force headed by the Director Criminal Investigations will undertake further investigations into other matters arising from this case."
Police were expected to release more information when there were new developments, Sakeo said.
DPP Pryde said the former PM and suspended police commissioner "are alleged to have arbitrarily and in abuse of the authority of their respective offices, terminated an active police investigation".
ACP Sakeo told local media the charges laid against them were not bailable.
He also defended the independence of the investigations.
"There is no interference into the handling of these cases by other senior officers, as the investigation team reports directly to me as their line Assistant Commissioner of Police, the Chief of Intelligence, Investigations and Prosecutions," he said.
"Investigators are given full autonomy to conduct the necessary work of the gathering of statements and evidence and the questioning of persons of interest."
'Everything under control'
Following the high profile arrests, police also put out a statement calling for calm.
"There is no reason to be concerned about public safety," police chief of operations Livai Driu said, adding that the country's "security landscape remains calm and manageable".
"No one should be apprehensive about the security of our nation, as Police have everything under control, and we urge everyone to go about their business as usual," he added.
Fiji's former Prime Minister Frank Bainimarama is taken into the Totogo Police remand centre in Suva on March 9, 2023. Photo: AFP / Leon Lord