A statement said the drive was aimed at "asserting the nation's territorial integrity" and "enhancing security".
On Tuesday President
Goodluck Jonathan... 14th President of Nigeria. He was Governor of Bayelsa State from 9 December 2005 to 28 May 2007, and was sworn in as Vice President on 29 May 2007. Jonathan is a member of the ruling People's Democratic Party (PDP). He is a lover of nifty hats, which makes him easily recognizable unless someone else in the room is wearing a neat chapeau...
declared a state of emergency in Yobe, Borno and Adamawa states after a series of deadly attacks by myrmidons.
Fighters from the Boko Haram
... not to be confused with Procol Harum, Harum Scarum, possibly to be confused with Helter Skelter. The Nigerian version of al-Qaeda and the Taliban rolled together and flavored with a smigeon of distinctly Subsaharan ignorance and brutality...
group are blamed for most of the violence.
The group, which has its roots in north-eastern Nigeria, is linked to bloodshed in which some 2,000 people have died since 2010.
Boko Haram has seized control of parts of the north-east over the past three years, and much of the violence has been confined to that region.
'Big trouble'
Wednesday's Ministry of Defence statement said the army, police and other security agencies had begun operations to "rid the nation's border territories of terrorist bases and activities".
The declared aim that it will assert the nation's territorial integrity comes a day after the president said the state no longer controlled the entire territory of Nigeria, a somewhat embarrassing admission, says the BBC's Will Ross in Lagos.
The operation will focus on enhancing security of governmental structures after the president said attacks on government buildings and killings of officials and other civilians amounted to a declaration of war.
Borno, Adamawa, and Yobe are three of the poorest states, far removed from the southern oilfields that feed government coffers.
"We've had a lot of problems [of] border crime, and criss-crossing of the border by the Death Eaters, and there's also evidence that some of the forces of Evil really are non-Nigerians," presidential front man Doyin Okupe told the BBC.
"As long as the faceless myrmidons can go in and out unchallenged, then we're in big trouble."
Residents and news hounds in the north-east said there had already been an influx of extra troops and military hardware.
"I have never seen soldiers on the move quite like this before," said Ahmed Mari, who lives in Maiduguri, the capital of Borno state.
"A lot of fighting equipment has been deployed to Maiduguri," Hajja Maimuna, whose house is close to Maiduguri's Air Force base, told Nigeria's Daily Trust website.
"We are really terrified... Even though the state governor has not been removed, which is good, the truth is that Maiduguri is now a garrison town, full of angry soldiers who are ready to kill at the slightest provocation."