Burkina has been caught since 2015 in a spiral of jihadist violence perpetrated by rebels affiliated with the Islamic State group and Al-Qaeda, which are also hitting neighbouring Mali and Niger.
"A large number of Jama'at Nusrat al-Islam wal Muslimeen (JNIM) fighters attacked a military base, homes and Internally Displaced People's camps in the city Djibo, in the Sahel region, killing at least 40 civilians and injuring more than 42," the UN agency said.
The agency said attacks on civilians were "inexcusable and must stop" with those behind them apprehended and judged at a fair and independent trial.
It added that deliberate targeting of civilians constituted a "war crime".
Djibo, near the border area straddling Niger, Burkina Faso and Mali, has been besieged by jihadist groups active in the region for months.
Several convoys seeking to resupply the town have been attacked.
Burkinabe security force sources told AFP that jihadists had carried out a massive attack Sunday on an army post at Djibo and that the army had killed dozens of attackers.
The sources added soldiers had been killed but did not mention civilian casualties.
A security source told AFP the Djibo army post had been the "target of a sizeable jihadist attack perpetrated by armed terrorist groups", adding an unspecified number of soldiers "paid the supreme sacrifice to hold Djibo".
The source added the army had inflicted "heavy losses on the enemy".
Another security source put the number of attackers in the hundreds, saying they were beaten back when the army called in air support.
The source said the waves of assailants had arrived on motorbikes and pickup trucks and carried out an attack lasting more than three hours.
That source added that several dozen jihadist fighters had been "neutralised".
- Jihadists besiege Djibo -
The official Burkina Faso news agency AIB said "more than 400 terrorists (were) cut down during the counter-offensive of the Burkinabe Armed Forces against nearly 3,000 criminals who tried to seize the town of Djibo."
AIB added that the "horde of terrorists" had sought "to sow death and desolation in Djibo, before taking control of the city".
The Sahel region around the city is one of the worst-hit zones in Burkina Faso and has witnessed some of the bloodiest exchanges.
The country has been run since September last year by a military junta led by Ibrahim Traore, who led the country's second putsch in eight months.
The military rulers have made the fight against the jihadist groups who control around 40 percent of the country their top priority.
The past eight years have seen the nation riven by a widening spiral of violence also experienced by neighbouring Mali and Niger, both of whom have seen their own military coups in the past three years.
The violence in Burkina Faso has displaced more than two million people and left more than 17,000 dead, civilians and army included, with some 6,000 killed so far this year according to NGO ACLED, which collects real-time data on reported political violence.
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