In a statement, the army said its forces were carrying out raids in one refugee camp in Arsal, in eastern Lebanon, when unknown attackers tried to set fire to tents in another neighbouring camp.
"Three attackers on a motorbike attempted to set fire to the other camp, so army forces opened fire on them, killing one and wounding the others," the army said in a statement.
The statement gave no further details about the fire, but activists circulated photos on social media showing thick black smoke rising from a destroyed campsite in the area.
Local residents, including a local official who spoke on condition of anonymity, disputed the army's story.
"Troops poured gasoline on the tents and then set fire to the camp," he told AFP.
"They attacked the women and children, and rounded up the men. They detained hundreds of men.
"I was just there, and I saw an old man, around 90 years old, with all his bones broken from the beatings," he added.
"There is no safety for the refugees in Arsal at all."
An army spokesman rubbished those claims as "lies" and repeated the details of the military's statement.
"Our troops act in accordance with international standards of humanitarian treatment," he told AFP.
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The UN refugee agency UNHCR had no comment.
Local residents said refugees staged a demonstration to protest the incident.
Lebanon's official National News Agency said "dozens" of Lebanese and Syrian citizens were arrested in the raids that began in the early hours of Thursday morning.
Among them, it said, were four gunmen from Al-Qaeda's Syrian affiliate Al-Nusra Front.
Tensions have been running high in Arsal since an incursion into the eastern Lebanese town on the border with Syria by jihadists last month.
Clashes broke out between jihadists coming from Syria and the Lebanese army, with the militants taking hostage several dozen soldiers and policemen.
The militants took the hostages with them when they withdrew from the town after a truce, but negotiations to free the men have gone nowhere.
Jihadists have so far executed three of the hostages, causing deep anger and anxiety in Lebanon and leading to a backlash against Syrian refugees in some places.
Aid groups working with refugees say there has been an uptick in attacks on Syrians, and the army was recently forced to distance itself from soldiers shown in a video kicking and beating Syrian men, including an amputee.
There are more than 1.1 million Syrian refugees in Lebanon, which has just four million citizens.