THE HAGUE, Oct 19 (Reuters) - The deputy prosecutor of the International Criminal Court (ICC) called on Friday for more cooperation in arresting suspects as she welcomed the transfer of a former Congolese militia leader to face war crimes charges.

"Perpetrators must know they will be prosecuted," deputy prosecutor Fatou Bensouda told a news conference.

"We rely on the continuing cooperation of states to help implement the court's arrest warrants, whether they are in the DRC, Uganda, Darfur or anywhere else," she said. "There is no excuse not to execute the court's warrants".

Kinshasa handed over Germain Katanga, a militia leader in northeastern Democratic Republic of Congo, to the ICC on Thursday, making him the second suspect to face justice at the world's first permanent war crimes court set up in 2002.

Katanga will have the opportunity to enter a plea when he makes an initial appearance in court on Monday.

The court has also indicted two people for war crimes in Darfur, one a Sudanese minister and the other a militia leader, as well as four leaders of Uganda's Lord's Resistance Army, but Sudan refuses to make arrests and the Ugandans are on the run.

The only other suspect surrendered to the court so far is Congolese militia leader Thomas Lubanga, whose trial is expected to get under way in the coming months.

Human rights groups have urged the court to extend its investigation to more senior military and political figures behind violence in the Democratic Republic of Congo.

Bensouda said the prosecution expected to issue more arrest warrants and rejected suggestions the court had only indicted Katanga because he was already in custody in Kinshasa.

"Whether he is a small fish or not, our mandate is to go for those who bear the greatest responsibility and we see Germain Katanga as one who bears the greatest responsibility for the crimes that we have charged him with," she said.

She said at least 200 civilians died when Katanga's militia went on an "indiscriminate killing spree" in Bogoro village in September 2003. Survivors were imprisoned in a building filled with corpses and women were sexually enslaved.

Katanga, 29, led the Patriotic Resistance Force in Ituri (FRPI) militia, which fought the Union of Congolese Patriots (UPC), led by the court's other detainee, Lubanga.

The two are being held at an ICC detention centre in a Dutch prison near The Hague. Court registrar Bruno Cathala said they could be separated if the prosecution requested it or if there were conflicts between the two former rivals.

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