Brigadier General Mosese Tikoitoga also defended the action of his troops in surrendering to the rebels, even though a contingent of 75 Filipino peacekeepers who defied an order to lay down their weapons all escaped unscathed.
Tikoitoga, speaking to reporters in Suva just hours after the UN Security Council demanded the Fijians' immediate release, said the location of the Blue Helmets was still unknown.
He also revealed that talks with their captors had hit a "lull" but said specialised UN negotiators flown in from New York to deal with the crisis had told him this was normal in a hostage situation.
"They (the rebels) do not establish contact so that they can regain the initiative on negotiations," he said.
"But these are (just) tactics they use and I hope that we will resume discussions soon and we can get them back on the line."
The fighters have made at least three demands, including that the al Nusra Front be removed from the UN's list of terrorist organisations.
Former Fiji prime minister Sitiveni Rabuka told Radio New Zealand on Wednesday that Fiji's Muslim community, which numbers about 60,000 in an overall population of 900,000, could face retaliation if the islanders serving with the UN were harmed.
"If anything should happen to the 45 then the unsuspecting and probably undeserving people who will bear the brunt of the feelings of the people could be the Muslim civil society and community in Fiji," he said.
Tikoitoga said the Fiji military was committed to treating all citizens equally and accused Rabuka of inflaming ethnic tensions.
"It's very irresponsible and I think it's closing in on inciting violence in Fiji. We should condemn it... it only shows the sick attitude of that individual," he said.
"The RFMF (military) will look after all Fijians and we don't hold anything against any Fijians for what's happening. This is a time we should all stand together, it is not the time to start pointing fingers at each other, especially internally."
Asked why his men surrendered, Tikoitoga said they were following a direct order from the commander of the UN Disengagement Observer Force (UNDOF).
"At no stage in an operation would I expect any of my officers not to follow the decisions of the first commander," he said. "The Filipinos chose to do so and the Philippines government have supported them for having chosen that path.
"We cannot criticise them for it, nor can we follow the decision they have made, we live by our own ethos of following command."
He said officers on the ground had to make a snap decision in a fraught situation.
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