Soldiers backed by heavy weaponry and fighter jets deployed after a dawn raid on the nearby village of Jintilo that prompted the authorities to put the entire city on lock-down.
Fears have been growing about a possible strike on Maiduguri since Islamist militants began seizing towns and villages in three northeast states about six months ago.
On January 3, they captured the fishing hub of Baga, in the far north of Borno State, which security analysts said put them in a better position to strike south to hit the state capital.
Others fled to Maiduguri, where many of the hundreds of thousands of displaced have sought sanctuary from the relentless wave of attacks and abductions.
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Last week, hundreds more fled four villages about 40 kilometres south of Baga after a warning from the militants, indicating a clear plan to push south.
Nigeria's military announced news of the raid on its Twitter account, saying: "Troops are repelling a simultaneous attack on Monguno and Maiduguri by terrorists."