The Director, Defence Information, Maj.Gen. Chris Olukolade, said this on Tuesday while featuring on a programme, entitled Focus Nigeria on the African Independent Television monitored in Lagos.
Though he admitted that the onslaught was at a cost to the media, it would not stop until the military was satisfied that none of the circulating vehicles of the media organisations was not being used to carry arms and ammunition for the insurgents.
He, however, pleaded for understanding, saying the media must consider the military action as one of the sacrifices that should be made for national security.
Olukolade denied media reports that the drivers of the media circulation vehicles were being detained and that newspapers were being confiscated.
But the Nigeria Labour Congress has said that the ongoing harassment of media houses in the guise of searching for dangerous materials was unacceptable under democratic governance.
The President of the NLC, Mr. Abdulwahed Omar, said the "seizure of newspapers, arrest of circulation drivers of several newspaper publishing companies as well as depriving the reading public access to information by operatives of the Nigerian military and other security agencies is absolutely unacceptable and clearly out of place in any democratic society" in an electronic mail on Tuesday.
Omar said that the military lacked the powers to trample on the freedom of the press and other freedoms entrenched in the constitution.
He stressed that the military also lacked the right to limit press freedom as the congress could not find a link between insecurity and a free press in a democratic regime.
He challenged the military to provide evidence of the involvement of the media in the violence and killings in the country.
Omar said that the media remained a critical organ for democratic development, stressing that any move to suppress the media and its operations as shown by the disruption of newspapers circulation would be resisted by the congress.
"The military and all the security agencies ought to know that all fundamental rights are germane to democracy and therefore lack constitutional and legal rights to unilaterally order the circumscription of freedom of the press or any freedom in any form as we cannot find the link between insecurity and a free press in democratic governance.
"There is an urgent need to prove the culpability of the news media in the ongoing violent attacks against people and critical facilities in Nigeria.
"For us, we strongly believe a free press is very critical in the sustenance of democracy and any obstruction to the operations of any critical organ of our democratic process would be resisted as the recent infringements in the circulation of newspapers portend," he added
Omar challenged the military to go after those threatening the sovereignty of the country whose violent activities had "almost disappointingly overwhelmed those paid to protect lives and property, despite huge budgetary allocations."
The labour leader said that the foreign media organisations seemed to have access to more information on the activities of the Boko Haram than the nation's security agents.
"In any case, foreign media organisations seem to have more access to information on these violent groups, especially Boko Haram, than our security agents.
"The military and other security agencies must restrict themselves to the protection of our sovereignty and go after those threatening this country with violent attacks that have almost disappointingly overwhelmed those paid to protect lives and property, despite huge budgetary allocations," he added
Omar noted that it was impossible for democracy to survive in Nigeria without the media and warned that the era of impunity associated with military dictatorship should not be resurrected under a democratically elected government.