“Information on social media would have people believe there was an army takeover,” government spokesman Alkassoum Maiga said in a statement.
“The government, while recognising the validity of shootings in some barracks, denies this information and calls on the population to remain calm.”
The gunfire came after a day after clashes between police and demonstrators during banned protests against the authorities’ failure to stem the jihadist violence ravaging the West African country.
It also follows the arrest earlier this month of numerous soldiers over a suspected plot to “destabilise institutions” in the West African country, which has a long history of coups.
“Since 1 am, gunfire has been heard here in Gounghin coming from the Sangoule Lamizana camp,” said a soldier in the district on Ouagadougou’s western outskirts on Sunday.
Residents there also spoke of “increasingly heavy fire”.
Shots were also heard at another military camp, Baby Sy, in the south of the capital, and at an air base near the airport, military sources said.
There was also gunfire at barracks in northern towns of Kaya and Ouahigouya, residents there told AFP.
The gunfire follows the country’s most recent protests against intractable jihadist bloodshed.
Police used tear gas to disperse protesters in rallies across the country on Saturday, arresting dozens. The authorities earlier in the week said they were banning the protests for security reasons.
Security sources reported that two soldiers were killed after their vehicle drove over a makeshift bomb in the north on Saturday.
In Kaya, residents told AFP that protesters had stormed the headquarters of the ruling party.
Groups linked to Al-Qaeda and the Islamic State group have plagued the landlocked Sahel nation since 2015, killing about 2,000 people, according to an AFP tally.
Attacks targeting civilians and soldiers have become increasing frequent — and are largely concentrated in the country’s north and east.
The jihadist violence in recent years has forced around 1.5 million people to flee their homes, the national emergency agency says, and many have settled in the region around Kaya.
On November 27, hundreds demonstrated against the failure of President Roch Marc Christian Kabore to quell the jihadist violence, sparking clashes with security forces that wounded dozens.
Those protest came days after an ambush by suspected jihadists targeting civilians and the VDP, an official self-defence force, in the northern You region left 41 people dead, including Ladji Yoro, considered a leader of the VDP.
Among the soldiers arrested this month over the plot to “destabilise institutions” was Lieutenant-Colonel Emmanuel Zoungrana, who had been commanding anti-jihadist operations in country’s badly hit western region.