Militants from Islamic State West Africa Province (ISWAP) stormed the base just before dawn in the Borno state town of Rann, near the border with Cameroon, a military officer told AFP.
"Four soldiers were killed and five others injured in the attack by ISWAP terrorists on the military base," the officer said.
The officer, who asked not to be identified because he was not authorised to speak on the raid, said the attackers seized weapons and military vehicles and took "several" soldiers hostage.
Ari Kime, a Rann resident, put the toll at five soldiers killed and six wounded.
The jihadists "snatched three gun trucks before leaving the base," Kime said.
ISWAP and the rival Boko Haram have intensified attacks on military bases in recent weeks.
Rann is the tenth base to be attacked by jihadists in the last two months, according to an AFP tally.
On Monday ISWAP militants raided a base in Marte, killing four troops and taking many others hostage before stealing weapons, according to military sources.
Since 2019, soldiers fighting the jihadists have shut down some smaller army bases and moved into larger garrisons in an attempt to better resist militant attacks.
However the attacks have intensified.
Around 100 people, including soldiers, were killed in various jihadist attacks in the northeast of the country in April.
- Overstretched military -
Raids on military bases provide jihadists in the Sahel countries with at least 20 percent of their weapons, according to the UK-based Conflict Armament Research (CAR) which has studied jihadist weapons sources for a decade.
The uptick in raids on bases by jihadists in northern Borno underscores the weakness of the Nigerian military and the increasing strength of the militant groups, which are forging closer ties with jihadist groups in the wider Sahel region.
The military has been overstretched by years of operations to combat the security challenges facing the country, Africa's most populous with 230 million inhabitants.
Late on Monday, jihadists opened fire on a joint military and police patrol team in the town of Gajiram, 80 kilometres from the state capital Maiduguri, local residents said.
No details on casualties were immediately available.
Lately the jihadists have also resorted to planting mines on highways in northern Borno where they have a strong presence.
On Tuesday a mine-resistant military truck escorting a military commander hit a landmine along the highway between Rann and the commercial town of Gamboru, military sources told AFP.
The commander, who was unhurt, was returning to his base in Gamboru after inspecting the ransacked Rann base, the sources said.
State governor Babagana Umara Zulum condemned the surge in attacks, vowing he was "more determined than ever to support the military, security agencies, and our volunteer forces in the fight to end terrorism and insurgency".
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