In a statement released from his office in New York, Annan said he was "alarmed by the continued possibility of a coup against the legitimate government of Fiji".
The capital of Fiji, Suva, was reported calm on Wednesday.
A day earlier a heavy troop presence was seen on the streets as 3,000 military reservists were called up to bases across the country.
The feud between Qarase and Bainimarama goes back almost two years with the military commander accusing the prime minister of corruption. He is threatening to "clean up" the government if Qarase does not agree to a range of demands.
Qarase in turn has tried to have Bainimarama replaced, but failed to remove him last month after senior military officers rallied around their commander.
Before the meeting in Wellington, Bainimarama appeared to be sticking to his position, telling New Zealand's Radio Tarana his stance was non-negotiable.
"It's very simple. He comes with a 'yes' or a 'no' to our demands, full stop,'' he said.
For his part, Qarase, in an interview with another New Zealand broadcaster, said he saw some room for manoeuvre.
However, he added that some of Bainimarama's demands, such as dropping criminal charges against him and other officers, would mean the military was overruling other government bodies.
Such a position would be "a threat to our democracy", he told New Zealand's National Radio.