The sidelined police chief, Sitiveni Qiliho, is regarded as a close supporter of former prime minister Frank Bainimarama, who ruled the Pacific nation for 16 years after leading a 2006 military coup.
Prime Minister Sitiveni Rabuka, also a former coup leader, emerged victorious from the closely fought election -- but the powerful military has warned it views the scale and speed of his government's reforms "with growing concern".
The military has wide powers to intervene in politics under the constitution of Fiji, which has endured four coups in the past 36 years.
Qiliho had risked Rabuka's ire by calling in the military to enforce law and order in the aftermath of last month's election, claiming to have unspecified "intelligence" about "planned civil unrest".
Corrections service chief Francis Kean -- Bainimarama's brother-in-law -- was also suspended from his post, a Fiji government statement said.
The pair "were suspended effective immediately pending investigation and referral to and appointment of a tribunal", it said.
President Ratu Wiliame Katonivere issued the suspensions on advice from the Constitutional Offices Commission, which is responsible for appointing the police commissioner and other senior officials, the government said.
The new acting police commissioner, Juki Fong Chew, issued a statement "to assure all Fijians that the focus remains on ensuring the safety and security of all Fijians and visitors to our shores".
In a sign of Rabuka breaking with the pro-China policies of Bainimarama, he has reportedly said Fiji no longer needs a police cooperation deal with Beijing that was signed in 2011.
"There's no need for us to continue, our systems are different," Rabuka was quoted telling the Fiji Times on Wednesday.
"Our system of democracy and justice systems are different so we will go back to those that have similar systems with us," he said, apparently referring to countries such as Australia and New Zealand.
Under the memorandum of understanding, Fijian police had travelled to China for training while Chinese officers had also joined programmes in Fiji, it said.
The prime minister's office could not confirm the report.
In a statement responding to the comments, a spokesperson for the Chinese embassy in Fiji touted the two countries' warm ties and defended the cooperation pact as having "effectively enhanced Fiji's capacity building in related areas".
"We hope that the new Fiji Government can continue to regard China as a reliable friend and partner," the statement said.
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