Residents in Bama and a local lawmaker said some 400 troops, some of them without weapons or boots, fled after a military jet mistakenly bombarded the town’s barracks during intense fighting.
Nigeria’s military countered that it had pushed back the militants, who in recent weeks have moved from indiscriminate and retaliatory hit-and-run attacks to seizing strategic territory in Borno state.
Last week, militant fighters, blamed for killing thousands since 2009, overran the border town of Gamboru Ngala and previously seized Gwoza and declared it part of an Islamic caliphate.
Some analysts have predicted that by seizing territory, Boko Haram is seeking to encircle the state capital, Maiduguri, to make it the centre of a hardline Islamic state.
“Nigeria is losing control of large parts of the northeast region,” said Andrew Noakes, of the Nigeria Security Network of experts in a report that warned of potential knock-on effects.
“If Borno falls to Boko Haram, parts of (neighbouring) Yobe and Adamawa (states) can be expected to follow. Parts of Cameroon along the border area would also probably be overrun.
“Unless swift action is taken, Nigeria could be facing a rapid takeover of a large area of its territory reminiscent of ISIS’s lightning advances in Iraq.
“Such a takeover would likely be accompanied by a major humanitarian crisis, involving the movement of possibly tens or even hundreds of thousands of internally displaced persons.”
In Bama, Nigeria’s military seemed to have the upper hand when Boko Haram fighters launched a pre-dawn raid on Monday, with troops deployed to the town before an apparent bid to recapture Gwoza.
But local resident Yasir Zarami said that changed when the military jet bombarded its own troops in an account back by Borno senator Ahmed Zanna in an interview on BBC radio’s Hausa language service.
Nigeria’s military said on its Twitter account @DefenceInfoNG on Monday evening that it had pushed back the insurgents and added: “The claim concerning the Airforce isn’t true.”
Top brass followed up on Tuesday with another tweet, which stated simply: “#Victory.”
But the Bama raid — and reports of fresh fighting 130km north of Bama in Monguno, where there is a large military base — again raised questions about Nigeria’s ability to tackle the insurgency.
Some Nigerian soldiers stationed in Maiduguri recently refused to deploy to Gwoza in an apparent mutiny, claiming they lacked the weapons to tackle the better-armed insurgents.
Civilians have borne the brunt of the fighting and the UN refugee agency said on Tuesday that at least 9,000 Nigerians had fled to Cameroon and more than 2,000 to Niger in the past 10 days.
“The total number of Nigerian refugees in Cameroon now stands at some 39,000, according to local authorities,” UNHCR spokesman Adrian Edwards told reporters in Geneva.
“Niger is already hosting more than 50,000 forcibly displaced from Nigeria who have arrived in the country since May 2013; 1,500 have found refuge in Chad.”