"As soon as people heard the first gunfire they fled the city" of Kolofata, a local Cameroonian source told AFP.
"The gunfire was very heavy," said the source, adding that the military base is in an area where police, elite army, and local government premises are also located.
Police confirmed the attack but there was no immediate information on any casualties.
Boko Haram has seized dozens of towns and villages in northeast Nigeria in the last six months and now reportedly controls the border areas of Borno state with Niger, Chad and Cameroon.
The fighters of Boko Haram, which roughly means "Western education is forbidden", began sending growing numbers of fighters into neighbouring Cameroon last year.
More than 13,000 people have died in northeast Nigeria's conflict since Boko Haram launched its insurgency in 2009 and hundreds of thousands more have been made homeless.
Last month Cameroon sent warplanes into action against Nigerian Boko Haram fighters for the first time, after the large force of jihadists crossed the border and seized a military camp.
Kolofata has been a Boko Haram target on several occasions, notably last July when several people were killed.
Another 27 people, including the wife of a deputy prime minister, have been kidnapped, held for week and then freed.
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