The military confirmed the searches, but officers denied that the moves were designed to muzzle critics, even though at least two of the newspapers had published damning articles about the army in recent days.
Four dailies -- The Nation, the Daily Trust, the Leadership and Punch -- all said they were affected, while The Nation said soldiers stormed one of its circulation offices.
"One of the military men told us that they were acting on (an) order from above as there were allegations that newspaper circulation vehicles were being used to smuggle arms and ammunition," one of The Nation's distribution managers said.
Defence spokesman Chris Olukolade said the search "followed intelligence report(s) indicating movement of materials with grave security implications across the country using the channel of newsprint-related consignments".
Nigeria's military has been under sustained pressure, including in the media, over its response to the Boko Haram insurgency, which has claimed thousands of lives since it began five years ago.
Attacks by the Islamist militant group have increased, with the military apparently powerless to prevent the bloodshed, exacerbated by the kidnapping of more than 200 schoolgirls in April.
"As such, the military will not deliberately and without cause, infringe on the freedom of the press," he added, calling the search a "routine security action".
Nigeria's response to the mass abduction of the teenage girls has been criticised as slow and lacklustre, while a social media campaign has prompted greater international media scrutiny of the counter-insurgency.
On Tuesday, the Leadership daily claimed that 10 army generals and five senior officers had been court martialled and found guilty of assisting Boko Haram.
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