A purported spokesman for a Nigerian Islamist sect has dismissed an arms mop up exercise by soldiers in the restive city of Maiduguri as a ploy to disarm residents ahead of a suspected crackdown.

In a conference call with journalists in the northeastern city, a man identifying himself as a spokesman for the Boko Haram sect that has been behind strings of deadly attacks in recent months, called on the city's residents not to give in to what he called a trick by the military.

"I call on the people of Maiduguri not to give in to this deception because it will amount to mortgaging your freedom and your enemies will attack you with ease," said Abu Qaqa.

Qaqa has claimed to speak on behalf of the radical sect on several previous occasions but Boko Haram is believed to have a number of factions and several others have identified themselves as spokesmen as well.

"Your arms are your only protection and the aim of disarming you is to render you defenceless and hopeless when the military launches its planned attack on you," said Qaqa.

Soldiers from a special military unit deployed to end the violence in the city on Tuesday launched a house-to-house search for weapons following an October 31 deadline for residents to turn in weapons.

A military unit's spokesman, Lieutenant Colonel Hassan Mohammed, said they have recovered at least 1,000 firearms in the first 24 hours of the exercise as residents who had been afraid to declare their arms rushed to drop them off at various designated collection points or simply left them by the roadside.

Towns and villages near Maiduguri city, the epicentre of frequent gun and bomb attacks by suspected sect members in recent months, are also targeted in the arms clean-up operation.

Boko Haram has claimed responsibility for the August 26 UN bombing that killed at least 24 people in Abuja.