Fiji's military has staged night-time exercises to secure strategic areas of the capital, Suva, citing fears of "foreign intervention".
Cdr Bainimarama has been at odds with Mr Qarase for months
Troops fired flares and set up checkpoints in what military leaders described as a training exercise.
The move came amid warnings by Australia and other regional powers of an imminent coup in the Pacific nation.
But PM Laisenia Qarase, who earlier met the military's chief for talks, said he had been told no coup would take place.
Mr Qarase, who met with military chief Frank Bainimarama in New Zealand, said their talks had made substantial progress, and that he looked forward to further discussions.
He described the exercises as "routine".
'Show of strength'
Fiji has been tense for weeks amid a public stand-off between the two sides, with military leaders accusing the government of corruption and deceitfulness.
In a statement on Wednesday, Fiji's military said the exercises were being carried out to protect the country.
Armed soldiers took up positions in the capital
"The exercise is in anticipation of any foreign intervention and the Republic of Fiji Military Force is taking all precautionary measures," the statement said.
Troops in full combat dress began securing the centre of Suva at midnight on Thursday (1200 GMT on Wednesday) for three hours of planned operations.
Armed troops manned checkpoints while others took up positions close to key institutions such as the national parliament, Reuters news agency reported.
The military advised the general public to remain cautious when travelling into the centre of Suva, but urged them not to be alarmed by the exercise.
The Fijilive website reported that it was "business as usual" on the streets of the capital, with people still going to nightclubs.
But Mark Simpson, a web designer from Lautoka, told the BBC News website: "The general population is very nervous.
"These military exercises are ridiculous, crazy. But I have to say, there was a buzz in the air for the coup in 2000 - that same feeling is about now."
Cmdr Bainimarama has repeatedly threatened to overthrow the government, despite Fiji having been through three coups in 20 years.
The heart of the feud between the military and Mr Qarase's government lies in plans by the government to offer amnesties to those involved in a racially-motivated coup six years ago.
The proposal is bitterly opposed by Cmdr Bainimarama, who put down the coup, and who at one stage was forced to flee for his life.
Australia's Foreign Minister Alexander Downer said the situation remained worrying in Fiji, despite what he called a "helpful" meeting between the two men.
Australia also said a Black Hawk helicopter had crashed into the sea near Fiji as it tried to land on HMAS Kanimbla. One person had died and another was missing.
Australia sent three naval ships to Fiji earlier this month as a precaution in case its citizens needed evacuating.
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