Garba Shehu, senior special assistant on media to President Buhari announced this on Sunday night.
He tweeted:”The Federal Government has directed the military to vacate the premises of @daily_trust and the order has been complied with.
“Issues between the military and the newspaper as they affect the coverage of the war in the Northeast will be resolved through dialogue”, he added.
Media Trust, publishers of the newspaper confirmed that the siege was lifted at 9.30pm.
The Daily Trust had reported that its Maiduguri regional office was shut down by security operatives on Sunday and its editor, Uthman Abubakar and reporter Ibrahim Sawab arrested.
Later, the newspaper also said its head office in Abuja was also invaded and computers carted away.
In what appeared to be a coordinated operation, a little while later, the Lagos Bureau Office was reportedly taken over by a combined team military and police officers.
The Media Trust did not confirm the release of its computers, in the statement by Manir Dan-Ali, the editor-in-chief.
What appeared to have triggered the military wrath was a report in the Sunday edition of the newspaper, revealing military preparations for a massive war against Boko Haram in the North East.
Military sources told NAN that the report revealed too much and endangered the planned operation.
But in his statement, Manir Dan-Ali claimed: “We have not been told of the reason for the military operation against this newspaper but suspect it may have to do with the lead story of the Daily Trust on Sunday that dwelt on the military’s effort to retake some towns recently reported to have been lost to insurgents.
“Another clue is that during the invasion of our premises both in Maiduguri and in Abuja, the military men were asking for the reporters who wrote the story.
“Media Trust Limited condemns this unlawful act and calls on the military authorities to release the two reporters arrested in Maiduguri and return the dozens of computers that were taken from our newsroom.
“We also like to thank our colleagues in the media and all others who have been calling and supporting us in our hour of need.
“We also appreciate the efforts of some government officials who insist that there is a better way of handling relations with the media.”