(Adds British Foreign Secretary comment, paragraphs 9-10)

By Joe Bavier

GOMA, Congo, Jan 25 (Reuters) - Congolese Hutu rebels said on Sunday they had clashed for the first time with a Rwandan-Congolese force deployed to crush them and civilians expressed fears they would be caught up in the violence.

Democratic Republic of Congo's army said late on Saturday the joint force had killed nine rebels from the Democratic Forces for the Liberation of Rwanda (FDLR) in two days of fighting in North Kivu province.

Congo's United Nations peacekeeping mission has so far been unable to confirm the army's statement.

FDLR military spokesman Lieutenant Colonel Edmond Ngarambe said he was seeking information, but the FDLR had wounded an unknown number of Congolese and Rwandan soldiers in an ambush.

Congo's ethnic Hutus said they feared they might be unfairly targeted by the joint military operation.

"When they hunt down the FDLR, they are going to kill us as well, because we are Hutus and the FDLR are also Hutus," said a man in the North Kivu town of Rugari, asking not to be named.

Anneke Van Woudenberg, senior researcher with New York-based Human Rights Watch, said those fears were legitimate. "In past operations ... the distinction between combatants and civilians has not been respected, and many civilians have died," she said.

MONUC, the U.N.'s largest peacekeeping mission with around 17,000 troops mandated to protect civilians, has said it was not involved in the planning of the anti-FDLR operations.

British Foregn Secretary David Miliband said in a statement that all military operations should be coordinated with MONUC.

"The cooperation between the governments of DRC and Rwanda in strengthening the political process and addressing militias is to be welcomed," he added.

FDLR fighters are accused of killing civilians, mainly Tutsis, recruiting children, and using rape as a weapon during their 14-year presence in Congo.

NKUNDA ARRESTED

More than 600 Congolese villagers have already been slaughtered by Ugandan Lord's Resistance Army rebels fleeing a similar offensive launched last month by Uganda's army in the former Belgian colony's remote northeast.

The FDLR vowed to fight any attack.

"We will defend ourselves if they come into areas where we are. There will be fighting, of course," Ngarambe said.

The presence in eastern Congo of the FDLR, some of whom are responsible for the deaths of 800,000 Rwandan Tutsis and moderate Hutus during that country's 1994 genocide, unleashed a recurring cycle of bloodshed that continues to this day.

Rwanda has twice invaded its much larger western neighbour under the pretext of rooting out the rebels, sparking a 1998-2003 war that triggered a humanitarian catastrophe estimated to have killed 5.4 million people.

Congolese President Joseph Kabila's decision to allow Rwandan soldiers to pursue the FDLR within Congo has been touted by his government as a move to pacify the troubled east.

In exchange, Rwandan authorities on Thursday arrested Congolese General Laurent Nkunda, whose Tutsi-dominated rebellion continued to receive support from Kigali as recently as late last year, according to a U.N. group of experts.

Government officials in Kinshasa have said they are waiting for his transfer to Congo to face charges of war crimes. (Additional reporting by John Kanyunyu; editing by Daniel Magnowski and Elizabeth Piper)

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