Boko Haram have targeted the police, churches and drinking establishments in their bid to impose sharia law [AFP]

Nigeria's ministry of defence has said that it will investigate allegations that military personnel mishandled attacks by an Islamist group.

The announcement came after a woman was shot dead on Wednesday in clashes between members of the government's Joint Task Force (JTF) and youths in Biu, a town in the northeastern state of Borno.

The clashes erupted in response to a JTF operation that ended with the arrest of clerics and members of Boko Haram, an Islamist group.

The group had claimed responsibility for months of attacks in and around Maiduguri, the capital of Borno. Strikes mainly targeted the police, churches and drinking establishments.

Local residents said the actions of the military were unjustified and burned a church in protest.

Nigerian President Goodluck Jonathan established a committee to investigate violence by Boko Haram and reprisal attacks by the JTF.

In a statement on Wednesday, Defence Minister Bello Mohammed said: "Presently our Armed Forces are doing a very good job in the protection of lives and property of Nigerian citizens in the various theatres of internal security and peace keeping operations."

He also admitted that there are "a few bad eggs" among them and that plans were underway to "orientate" the armed forces to be more civilian-friendly.

Local Borno leaders claim that the military has done more harm than good in dealing with Boko Haram.

According to Amnesty International, police brutality, unlawful arrests, killings and disappearances have been carried out by authorities for months.

Thousands of residents fled Maiduguri in recent weeks, after clashes between JTF and Boko Haram intensified.

Violence by the group even reached the country's capital, where Boko Haram placed a bomb in the car park of national police headquarters.

Boko Haram wants to impose sharia (Islamic law) across the country - a goal most Nigerian Muslims do not support.