* Factions fight near Ugandan border
* Insurgent split complicates peace efforts
* Other armed groups profiting from confusion (Adds Ugandan official, UN military spokesman, details)
By Jonny Hogg
KINSHASA, March 1 (Reuters) - Thousands of Congolese civilians fled to neighbouring Uganda on Friday to escape clashes between rebel factions, one of them led by a renegade general wanted on war-crimes charges, witnesses said.
Fighting in eastern Congo spilled into a second day after the M23 rebel group's military command sacked the group's political leader on Thursday for his links with renegade Bosco Ntaganda, prompting fighters to turn their weapons on each other.
The violence risks exacerbating a humanitarian crisis. Nearly three quarters of a million people have fled their homes since the crisis began last year.
Around 4,000 residents of the border town of Bunagana began crossing into Uganda on Thursday after fighting broke out in the hills near the town, residents and officials said.
"They're currently camped in a temporary refugee camp. Most (of them) think the fighting won't last long but of course if the instability continues we can take these people to permanent resettlement areas," Moses Watasa, spokesman for the prime minister's office in Uganda said.
Light and heavy weapons fire continued through Thursday night and into Friday morning near Bunagana, as Ntaganda's men attacked positions held by M23's military commander Sultani Makenga.
"It's Makenga's men who control the town ... Most of the town has fled. I'm at home but my family has already left," a local community leader, Damien Batimaha, said.
Colonel Vianney Kazarama, a spokesman for M23, confirmed the fighting. "They (Ntaganda's men) organised an attack against General Makenga's headquarters at Chanzu - 11 km (7 miles) from Bunagana. He repulsed them throughout the night and they have fled, leaving lots of bodies and wounded behind," he said.
Despite a lull in clashes between the two factions later on Friday, UN peacekeepers stepped up their patrols as other armed groups took advantage of the confusion.
Eastern Congo has suffered nearly two decades of violence, with civilians regularly caught in the crossfire as a multitude of rebel groups and the country's poorly trained and corrupt army battle for control of land and mineral resources.
Other towns in the area - which has been under M23 control since last year - were pillaged by local militias and rebel groups as M23 soldiers pulled out, according to local sources.
"Rutshuru is in the hands of FDLR, they've been pillaging the shops," a businessman from the town said, in reference to the Rwandan Hutu extremist group active in eastern Congo for nearly two decades and blamed for committing some of the worst atrocities against civilians. He asked not to be named.
Several clashes between rival militias were reported by UN-backed local broadcaster, Radio Okapi, and a UN military spokesman confirmed there was increased armed group activity.
"The area was under de facto control of M23, and as soon as they left we've seen lots of movements from other armed groups trying to take advantage, that's why we've stepped up patrols," the UN peacekeeping mission's spokesman, Lt. Colonel Felix Basse, said.
Basse also said there had been intense movement of M23 fighters and equipment, with troops loyal to General Makenga heading north towards hills on the Rwandan border, whilst Ntaganda's forces were based near Kibumba, 30 km north of Goma.
A Reuters witness said troops loyal to Ntaganda were visible as little as 5km north of the town.
The power struggle within M23 ranks will further damage efforts to revive stalled peace talks hosted by Uganda, and may spur the Kinshasa government to push for a military solution to the recurring rebellions in the east.
Ntaganda - whose defection from the army in March last year helped spark the insurgency - is wanted by the International Criminal Court for alleged massacres during a previous revolt.
Separately, the UN said that around 3,000 people had crowded around their base in the town of Kitchanga, after clashes on Thursday between the Congolese army and fighters from a formerly pro-government militia, in which at least 26 died. (Additional reporting by Elias Biryabarema; Editing by Richard Valdmanis and Ruth Pitchford)