* Attacks take place two days after 59 killed in school siege
* Boko Haram biggest security threat in Nigeria
* President Jonathan struggling to stem insurgency (Adds Hollande, Nigerian military comment)
By Imma Ande
YOLA, Nigeria, Feb 27 (Reuters) - Gunmen from Islamist sect Boko Haram shot dead at least 12 people during a four-hour siege on villages in northeast Nigeria overnight, two days after a deadly attack on a school, witnesses said on Wednesday.
Boko Haram, whose fight for an Islamic state in northern Nigeria has killed thousands and made them the biggest threat to security in Africa's top oil producer, is increasingly preying on the civilian population.
Gunmen riding in 13 pick-up trucks sped into Kirchinga village in Adamawa state in the evening, burning churches and houses and shooting sporadically at fleeing villagers, residents said.
The insurgents chased residents into neighbouring Shuwa village, where they torched the house of a local bishop, a theological school and a police station.
The owner of a bakery, Martha Yakubu, said she counted 12 dead bodies, including two of her workers. Banks, small schools and dozens of houses were attacked.
The military said in a statement that six members of Boko Haram, one soldier and three civilians were killed in the fighting. Nigerian authorities often play down the military's own casualties and those of civilians, security sources say.
The villages are in a hilly region running along the Cameroon border where soldiers have struggled to pin down insurgents who hide in rugged terrain and launch guerrilla attacks on areas they accuse of being pro-government.
Boko Haram gunmen killed 59 pupils at a boarding school in Yobe state, in the northeast close to Adamawa, in the early hours of Tuesday, in an attack President Goodluck Jonathan called "callous and senseless murder".
Western governments are concerned about Nigerian groups like Boko Haram linking up with al Qaeda-linked cells in other countries in the Sahel region, like Mali, where France sent troops a year ago to oust Islamist militants.
"Today Nigeria is facing the terrorism of Boko Haram," French President Francois Hollande said on Thursday during the West African country's 100 year anniversary celebrations in the capital Abuja.
"I assure you...your fight is our fight and we will always be ready to not only give you political support, but our help every time it is necessary," Hollande added, without giving details of what help was on offer.
Jonathan's troops are struggling to stem Boko Haram's insurgency, although they have restricted attacks mainly to the country's remote northeast corner in recent months, far away from commercial capitals and southern oil fields.
Militants from Boko Haram, whose name means "Western education is sinful" in the northern Hausa language, have frequently attacked schools in the past. A similar attack in June in the nearby village of Mamudo left 22 students dead.
They have killed more than 300 people this month, mostly civilians, including in two attacks last week that killed around 100 each, one in which militants razed a whole village and shot panicked residents as they tried to flee. (Additional reporting by John Irish in Paris; Writing by Joe Brock; Editing by Angus MacSwan)
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