The regime led government yesterday put out a statement saying the Police Commissioner had resigned for personal reasons but Groenewald told the ABC it was because of military interference.
"For personal and family reasons, the Commissioner of the Fiji Police Force, Mr Bernardus Groenewald, has submitted written notification for an early release from his contractual appointment as the Commissioner of the Fiji Police Force with effect from Tuesday, November 10, 2015," a statement from the government said.
Land force commander Lieutenant Colonel Sitiveni Qiliho will replace Groenewald for three months until a new person is appointed to the role.
Groenewald said his resignation is "indirectly" related to a case of alleged police brutality involving escaped prisoner Iowane Benedito who was beaten with wooden and metal poles by three police officers.
Groenewald had been pushing for these three officers to be prosecuted for the beating but they were recruited by the military.
Land Force Commander Sitiveni Qiliho said the three suspended police officers were recruited because they were working for the safety of the people of Fiji and had been abandoned by the police.
"The fact is I don't agree with the way they're interfering with policing," Groenewald told Radio Australia's Pacific Beat program.
"I'm a true-blooded police officer and I'm not satisfied with the way that they're interfering in policing."
This blog revealed two years ago that the beating and torture was spearheaded by Bainimarama's task force and police team.
We revealed that the licence plate of the ute, believed to be a government vehicle, where Benedito was beaten and brutalized was FL541.
A police source had told us then that FL541 was a police task force vehicle previously used by the director of CID, which was then given to the drugs team and then the strike back team of the former commissioner of police, Ioane Naivalurua.
Groenewald served for more than 40 years in South Africa before accepting the role of Fiji police commissioner.