GENEVA, Sept 28 (Reuters) - Eleven thousand people have fled Mogadishu this month because of intensified violence and the northern part of the Somali capital is becoming increasingly deserted, the U.N. refugee agency said on Friday.

Northern Mogadishu is a stronghold of Islamist insurgents fighting Ethiopian troops supporting the transitional government in the Horn of Africa country.

"Our staff report that families are still fleeing Mogadishu every day due to an increase in violence," said Jennifer Pagonis, spokeswoman for the U.N. High Commissioner for Refugees (UNHCR). "In September alone, 11,000 people fled Mogadishu."

There were more departures this week after the government ordered residents of three northern districts to vacate their homes, she said. The government accused the residents there of supporting the insurgents.

"What we are seeing now is Mogadishu has become divided into two parts; the northern part is becoming increasingly deserted as residents flee clashes between the Ethiopian-backed TFG (transitional federal government) forces and insurgents, whereas the southern part of the city is calm," Pagonis said.

Bakara Market, which used to be one of the biggest in East Africa, was barely functioning and was often closed to vehicles because of fighting, assassinations and criminal killings, she said.

About 65,000 people have fled Mogadishu since the beginning of June, according to the UNHCR.

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