Violence has spread to the state capital Makurdi
Regional officials say that more than 200 villagers were killed by soldiers to avenge the murder of 19 comrades by tribesmen on 12 October.
The army, which is maintaining a heavy presence in the area and has imposed a dusk-to-dawn curfew, has denied all involvement.
But the BBC's Dan Isaacs, who is in the state capital Makurdi, says the army has clearly been meting out its revenge.
Latest eyewitness reports say the town of Zaki Biam, where the abducted soldiers were found hacked to death, has been largely destroyed by army shelling.
Troops first entered the town on Monday shooting at civilians before launching rocket-propelled grenades at buildings.
A local television crew visited the scene shortly afterwards and filmed graphic pictures of charred bodies lying in the streets.
There is also compelling evidence that people in the villages of Gbeji, Anyin and Iorja were rounded up, shot and their bodies subsequently set alight.
Attacks were also reported in the villages of Vaase, and Tseadoor.
Protests
Angered by the soldiers' action, university students took to the streets of Makurdi on Wednesday, burning tyre barricades.
At least 13 people were killed and three mosques set on fire in the Makardi protests on Wednesday, Reuters news agency quoted residents as saying.
A security adviser to the state governor visited Zaki-Biam on Wednesday told the BBC he had witnessed the systematic destruction of buildings by soldiers.
The town itself is now deserted.
Echoes of past attack
President Olusegun Obasanjo has yet to make an official statement on the Benue attacks.
But the BBC's Dan Isaacs say the unrest clearly demonstrates the fragility of civilian rule in Nigeria when tensions and divisions within the army can provoke such violence.
The governor of Benue has already called for troops to be withdrawn.
Soldiers were initially sent to track down the killers of the 19 soldiers, who were found hacked to death after being deployed to quell violence between two local tribes, the Tivs and Jukuns.
The Benue killings recall an earlier massacre in November 1999 when troops killed civilians and levelled the town of Odi in the Niger delta after a number of soldiers were abducted and killed.