Lt Col Shekari Galadima told the BBC the city was “very calm” as the army was enforcing a 24-hour curfew. He insisted there would be no more riots.
But a BBC reporter in the region says the violence has now spread to Pankshin town, 100km (60 miles) from Jos.
Rights groups say at least 200 people are believed to have died since Sunday.
Jos has been blighted by religious violence over the past decade.
At least 200 people were killed in an outbreak of fighting between
Muslims and Christians in 2008, while some 1,000 died in a riot in 2001.
Col Galadima told the BBC’s Network Africa programme that Jos city “has been brought under control tremendously”.
“Because of the 24-hour curfew imposed by the government, movement has been restricted so you cannot have any riots or any demonstrations going on,” he said.
“Our troops in combination with the police are fully deployed and fully on the ground to check all movements.”
The Associated Press reported that soldiers with machine guns were patrolled the streets of Jos in the back of pick-up trucks.
Residents were stopping and raising their hands to show they were not a threat as the trucks passed, according to AP.
The BBC Hausa service’s Shehu Saulawa says the violence appears to have spread much further than was previously thought – to the town of Pankshin.
He says reports claim public buildings in the town have been set alight, places of worship have been burnt and locals are appealing for the security forces to intervene.
Roadblocks have been set up on roads leading out of Plateau State and Christian and Muslim leaders have appealed for calm.
The Red Cross, which was unable to get into Jos on Tuesday, says its workers have begun to treat the wounded.
Rights groups have expressed fears that people are running short of food because they are confined to their homes as part of the 24-hour curfew.
And about 5,000 people have fled the violence and are using army barracks and public buildings as temporary accommodation.
The Jos-based League for Human Rights said people have little faith in the security forces to restore order.
The group’s Shamaki Gad told the BBC that no-one had been prosecuted for participating in previous religious and ethnic clashes.
Jos is in Nigeria’s volatile Middle Belt – between the mainly Muslim north and the south where the majority is Christian or follows traditional religions.
Correspondents say such clashes in Nigeria are often blamed on sectarianism.
However, poverty and access to resources such as land often lie at the root of the violence.
It is unclear what the trigger was for the latest bout of violence.
Plateau State spokesman Dan Manjang told Network Africa there were reports that it may have started after a football match.
But he said it would be surprising if football was the reason.
Reuters quoted residents as saying the violence started after an argument over the rebuilding of homes destroyed in the 2008 clashes.