Gunfire was heard coming from the barracks at Korhogo, a city in the north of the country, at around 1:00 am (0100 GMT), Adama Coulibaly, a local carpenter reached by phone said.
"There are three dead soldiers," an officer told AFP separately, without giving further details.
A source at the local morgue said three bodies in military fatigues and with gunshot wounds had been taken to the facility.
In a separate incident, shooting was heard from a former UN base near Abidjan, lasting from about 1.30 am to after 3:00 am, a local resident in the nearby district of Abobo said.
The incident takes place against a backdrop of months- long tensions within the country's armed forces.
The former French colony suffered a decade-long civil war, splitting the country in two.
Thousands of rebels were then incorporated into the army after President Laurent Gbagbo was ousted in 2011 by Alassane Ouattara.
But a string of revolts erupted from January to May this year after they mutinied to press demands for a promised bonus. They eventually received a payoff of 12,000 CFA francs (18,000 euros) per head from the state.
Four of them were shot dead in May when security forces intervened to disperse a protest.
And on Tuesday, two former rebel leaders who obstructed a road in the central city of Bouake were jailed.
The government last year unveiled plans to modernise the 22,000-man military, part of which would involve the departure of several thousand men, particularly ex-rebels.
But falling cocoa prices have severely crimped the government's coffers.
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