At one compound housing the police tactical unit troops were reported to have begun removing weapons and loading them onto a military truck.
However police officials denied the army had taken control of the facility.
"The army asked to examine what weapons this unit has. It is not violent," Moses Driver, the assistant police commissioner, told Fiji radio.
"It is a just a friendly visit," Driver said. "There is no confrontation of any sort."
One of the military’s key demands has been the disbanding of the police tactical unit – the only part of the Fijian police force allowed to carry weapons.
On Friday Bainimarama said Qarase had missed a deadline to agree to military demands, adding that he had taken that as a green light to go ahead with a "clean up" of the country’s government.
Bainimarama has said any take over would be peaceful, but has warned neighbouring countries – particularly Australia and New Zealand – to stay out of Fiji’s internal affairs.
Earlier on Monday more than 100 soldiers in battle uniform paraded inside the military's Queen Elizabeth Barracks headquarters on a hilltop overlooking Suva.
About five trucks full of soldiers later left the barracks in the direction of Suva's airport but there were no signs the military had begun taking control of the capital.