At the northern edge of this city’s sprawling military base, a vast field of churned soil conceals the hidden toll of a deadly offensive by the allies of Islamic State.
After dark, the bodies of soldiers are covertly transported from a mortuary that at times gets so crowded the corpses are delivered by truck, according to Nigerian soldiers, diplomats and a senior government official. The bodies are laid by flashlight into trenches dug by infantrymen or local villagers paid a few dollars per shift.
“Several of my comrades were buried in unmarked graves at night,” said a soldier from the Maimalari barracks, where more than 1,000 soldiers are based. “They are dying and being deleted from history.”
The secret graveyard at Maimalari isn’t the only one in Nigeria’s troubled northeast, the senior government official said.
The burials convey a picture at odds with a war Nigerian President Muhammadu Buhari, a former general, has repeatedly claimed his army has won.
The reality is that Africa’s largest land force—a U.S. counterterrorism ally—is struggling against an insurgency that first flared a decade ago and is now rejuvenated by Islamic State and the return of fighters from Libya, Syria and Iraq.
The insurgents now control hundreds of square miles of territory across four countries around the Lake Chad basin, a crossroads of Africa where U.S., U.K. and French militaries have bases or provide special-forces training. On Sunday, gunmen attacked a funeral on the outskirts of Maiduguri, killing at least 65 people, according to government officials.
“This group is one of the most effective, if not the most effective Islamic State contingent at the moment,” said Site Intelligence, a terrorism-monitoring group.
Nigeria’s government last summer stopped reporting the deaths of soldiers in its fight with Boko Haram insurgents and a splinter group that calls itself Islamic State West Africa Province. Mr. Buhari was re-elected in February after a security-focused campaign in which he repeated that Islamist insurgencies in Nigeria had been “technically defeated.”
But the sprawling secret graveyard in Maiduguri and an official cemetery at the base, the operational command for the northeastern front in Borno State, now hold the bodies of at least 1,000 soldiers killed since the terror groups began an offensive last summer, according to soldiers and military officials—some of whom estimated a far higher death toll.
The Nigerian military and the presidency didn’t respond to requests for comment on the war, casualties and the secret cemeteries.
In November, Mercy Tamuno was told her husband, Adah, had been killed in an insurgent attack on an outpost in Cross Kauwa, a town about 100 miles north of Maiduguri. When she demanded to see where he was buried, she was taken to the official cemetery at Maimalari, where graves are marked with plywood headstones. There she was led to a spot marked with a plastic bottle with her husband’s name written on it.
“It was the only one marked in this way. I’m not sure it was his grave but that’s what the army told me,” Mrs. Tamuno said.
Two soldiers from Lance Cpl. Tamuno’s unit said he had been buried days earlier in the secret graveyard. The plastic bottle was prepared to appease his wife, they said.
“We know he was buried in the unmarked grave. There was no funeral,” one said.
As the secret cemetery at the Maimalari barracks grows, the military has expanded the site into neighboring fields. “The farmland has been fenced off so they can bury the forces,” said Sarah James, a 50-year-old farmer whose husband is a retired soldier.
Official secrecy and a weak economy have left Nigerian soldiers poorly equipped to fight. Soldiers who would ordinarily rotate out every few months have been on active operations for years. Morale is collapsing and discipline beginning to fray, said soldiers and the senior government official.
Videos reviewed by The Wall Street Journal show Nigerian troops doling out gruesome punishments to suspected jihadists. The videos, which show dismemberment and killing of suspects, suggested the troops were suffering from trauma and needed human-rights training, said David Otto, director of security firm Global Risk International.
Units that have suffered casualties and declining morale aren’t in a position to attack, and are instead defending poorly constructed bases in exposed areas against an increasingly well-equipped enemy.
“There is a systemic misrepresentation of the war that is having severe tactical and operational consequences,” said Chidi Nwaonu, a former Nigerian soldier who now runs a security consulting firm, Vox Peccavi.
He said the bravery of troops was being undermined by poor decisions of senior commanders. “It’s part cock-up, part conspiracy,” he said.
The rapid rise of the Nigerian Islamic State spinoff, known as ISWAP, begins a new chapter for the jihadist movement after its defeat in Syria and Iraq, Nigerian and Western officials said. The group has an estimated 5,000 fighters who have established themselves in the borderlands around Lake Chad, where they are enmeshing themselves into communities, controlling trade routes, taxing the fishing industry and imposing an extremist brand of Islamic justice.
Islamic State commanders advised them to focus attacks on security forces, in contrast to Boko Haram, which has deployed hundreds of suicide bombers and shot to prominence in 2014 by kidnapping 276 schoolgirls. ISWAP usually attacks at night, when Nigerian air power is less effective.
President Trump has offered additional U.S. support for Nigeria’s military. U.S. experts are training Nigerian bomb squads and the U.S. in November awarded a $329 million contract to Sierra Nevada Corp. for 12 A-29 light attack aircraft for the Nigerian Air Force, with a completion target of 2024.
Western military officials say the Nigerian army is stretched so thin that its top brass are no longer talking seriously about defeating the insurgency, merely containing it.
In a video released by Islamic State in June, insurgents pose in front of seized tanks, armored personnel carriers and naval vessels, and warn government forces to repent “before we catch you.” The video shows militants killing four Nigerian soldiers by firing squad and another by rocket-propelled grenade.
Soldiers are barred from speaking to the media and some unit commanders don’t report deaths to preserve their scant budget allocations, soldiers and diplomats said.
But news is starting to leak out through social media. After an attack in November on the army base in Metele, perched on the border with Niger and Chad, a five-minute video circulated among soldiers showing the aftermath. Over images of smoldering tanks and armored vehicles, a narrator laments the quality of military equipment the base was given.
“See the weapons they bring here. These are not working,” he says. “No less than 100 plus soldiers died here. Many are missing in action, they are nowhere to be found.”
Nigeria’s military initially refused to comment on the attack. After questions from the senate, the military said 23 soldiers had been killed. It said false casualty figures and the sharing of inaccurate videos were boosting the “propaganda intent of the terrorists.”
When Timothy Olanrewaju, a journalist based in Maiduguri, couldn’t reach his brother, Sgt. Samuel Olanrewaju, for four months, commanders repeatedly assured him that his brother was well, stationed in a sensitive combat zone.
Mr. Olanrewaju learned of his brother’s fate when Islamic State published a video that showed his execution. Several hours later, he was still in shock, slumped on a mattress in his living room, struggling for words. “I couldn’t believe my eyes,” he said. “Why didn’t they tell me the truth?”
The military’s secrecy about casualties is so widespread it is unclear whether Nigeria’s political leaders are aware of the state of the conflict.