Computers were seized and two journalists in the northeast city of Maiduguri were detained following the Daily Trust story about military plans to recapture the town of Baga on the shores of Lake Chad.
The army said it acted because the newspaper had compromised national security by publishing details of future operations against the jihadists.
Soldiers and operatives from the secret police and civil defence paramilitary raided the daily’s offices in Maiduguri, the capital Abuja, and commercial hub, Lagos, on Sunday.
Army spokesman Brigadier-General Sani Usman said the report “divulged classified military information, thus undermining national security”.
He alleged it gave the Islamist extremists “early warning” and as a result “sabotaged the planned operations… putting the lives of troops in imminent and clear danger”.
Usman, who has previously threatened the media with legal action for publishing unofficial information on the violence, said the action was conducted in good faith.
Operatives had only wanted to “invite” those behind the report to discuss its implications, he added in a statement late on Sunday.
Daily Trust editor Mannir Dan-Ali condemned the action as “unlawful” and said the stand-off at the newspaper’s Abuja headquarters lasted five hours.
President Muhammadu Buhari ordered an end to the newspaper office siege, his spokesman said, which provoked strong condemnation on social media and comparisons to media repression under decades of military rule.
Some commentators compared the action to harassment of the media and censorship during former army general Buhari’s previous time as military head of state in the 1980s.
In 2018 Nigeria ranked 119 in Reporters Without Borders’ global press freedom index, a notch lower than war-torn Afghanistan.
The Africa Program Coordinator at the Committee to Protect Journalists, Angela Quintal, said the army’s raid of the Daily Trust was “outrageous” and a “blatant violation” of media and citizens’ rights.
Amnesty International Nigeria said the authorities had an “obligation to protect freedom of the press… as provided by the constitution and international human rights laws”.
The Daily Trust was one of four newspapers that were targeted under the previous administration of president Goodluck Jonathan in 2014 after publishing articles critical of the military.
The newspaper last week reported that Boko Haram, which the government has repeatedly said is on the verge of defeat, had captured six locations in northern Borno state, including Baga.
The claimed seizure came after months of attacks on military bases in the remote region blamed on or claimed by the Islamic State-backed faction of Boko Haram, ISWAP.
More than 27,000 people have been killed in the violence since 2009 and more than 1.8 million remain homeless.