KHARTOUM (Reuters) - Thousands of people protested in Khartoum on Friday after preachers condemned an International Criminal Court arrest warrant for Sudan's president on charges of war crimes in Darfur.

It was the third day of demonstrations after the Hague-based court announced it was indicting President Omar Hassan al-Bashir on seven counts of war crimes and crimes against humanity, including murder, rape and torture.

Up to 2,000 people massed outside the headquarters of the European Commission in Khartoum and hundreds of others were seen gathering outside mosques in other parts of the city.

Crowds shouted down, down USA and down, down ICC as mosques emptied after Friday prayers. There was a heavy security presence on the streets, but the protests appeared much smaller than the mass rallies supporting Bashir in Khartoum on Thursday.

Preachers in a number of Khartoum mosques gave sermons calling on Muslims across Sudan to condemn the ICC decision.

Sudan is refusing to deal with the court and this week expelled 13 high-profile aid agencies, including Oxfam and Save the Children, from the north of the country accusing them of passing evidence to the court.

The agencies deny dealing with the court.

U.N. humanitarian agencies said the expulsions threatened the lives and health of millions of people. U.N. officials suggested it could be a breach of international law. [nL6685622]

U.N. Secretary-General Ban Ki-moon has called on Bashir to reconsider the move, saying the non-governmental organizations (NGOs) help 4.7 million people in Africa's biggest country.

To knowingly and deliberately deprive such a huge group of civilians of the means to survive is a deplorable act. Humanitarian assistance has nothing to do with the ICC proceedings, U.N. human rights spokesman Rupert Colville said.

To punish civilians because of a decision of the ICC is a grievous dereliction of the government's duty to protect its own people, he told a news briefing.

NO FOOD, WATER, MEDICAL CARE

Of the 76 NGOs in Darfur with which the U.N. is working, the 13 that have been expelled account for half the aid that is distributed in the region, said Elisabeth Byrs, spokeswoman for the U.N. Office for the Coordination of Humanitarian Affairs.

Their departure would leave 1.1 million people without food, 1.5 million without medical care and more than one million without drinking water, she told the briefing.

It will be very, very challenging for both the remaining humanitarian organizations and for the government of Sudan to fill this gap, she said.

Aid officials said some workers from expelled agencies had been searched and harassed by Sudanese security officers since pulling back to their headquarters in Khartoum on Thursday.

It has been quite serious, quite nasty. They have been checking under mattresses, looking in cupboards. said one aid worker who asked not be named. Computers and files were seized but no one had been arrested, officials said.

MSF International President Christophe Fournier told a news briefing: We do not cooperate nor give any information to the International Criminal Court.

Fournier, a French medical doctor, said the expulsion of the French and Dutch MSF units would make it difficult for the remaining workers from MSF Spain, Switzerland, and Belgium to provide life-saving aid.

The U.N. refugee agency UNHCR fears the loss of aid within Darfur could prompt a mass influx of refugees into neighboring countries, such as Chad.

The head of Sudan's state Humanitarian Aid Commission, Hassabo Mohamed Abd el-Rahman, has said civilians will not be affected as the work of the expelled agencies will be taken up by the government and remaining humanitarian groups.

The founder of the rebel Sudan Liberation Army (SLA), Abdel Wahed Mohamed Ahmed al-Nur, said the departure of the aid workers was a disaster for the people of Darfur.

But Nur said the arrest warrant did offer new hope because it would dissuade attacks by government troops and proxy militias.

Nur's SLA and another rebel group took up arms in 2003, accusing Khartoum of neglecting the development of Darfur. Sudan used government war planes and proxy militias to crush the rebellion. International experts say the conflict in Darfur has killed 200,000 people and displaced 2.5 million.

(Additional reporting by Jonathan Lynn and Laura MacInnis in Geneva; Editing by Janet Lawrence)

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