The violence has led 1.5 million people to flee their homes
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Sudan's government has defended the forcible relocation of refugees from camps in the western Darfur region.
Humanitarian Affairs Minister Ibrahim Mahmoud Hamid said it was the act of a responsible government to move them to a better location.
Earlier, the UN said called the action a violation of humanitarian law.
On Tuesday Sudanese forces sealed a number of camps in southern Darfur and moved some of their residents. Some say they were beaten up.
More than 1.5 million people have fled their homes in the region and some 70,000 have been killed in the conflict.
Pro-government Janjaweed militias are accused of driving the region's black Africans from their villages, since two rebel groups began an uprising in February 2003.
Scorching sun
The Sudanese government has been stung by criticism from UN Secretary-General Kofi Annan, the BBC's Jonah Fisher in Khartoum says.
Mr Hamid said the relocation of the refugees had not violated any humanitarian agreements.
"It is the responsibility of the government to move them to a suitable place," he told the BBC's Focus on Africa programme
In El Geer camp 250 families were moved onto police trucks early on Tuesday.
The BBC's Alexis Masciarelli said they were now trying to shelter from the scorching sun outside another camp, El Suaref.
Return fear
Their community leader said they now fear being forcibly sent back to their village, which they fled after attacks by Janjaweed militia.
But Mr Hamid said there was no move by authorities to force the refugees to return to their villages.
And he denied refugee claims of police brutality, saying: "It is the responsibility of the police to protect the people."
The Khartoum government said it had to intervene in the camp because they had received reports of fake refugees trying to take advantage of aid distributions.
The humanitarian effort in Sudan is being hindered by rising tension between rebel groups and Arab militiamen.
A senior African Union (AU) official in Sudan said the ceasefire agreed in April, was being violated every day by both sides.
However AU negotiators in the Nigerian capital, Abuja, have said that they are hopeful that all parties will sign an agreement they have drawn up to resolve the 20-month conflict
The agreement states that all parties must tell the ceasefire commission exactly where their troops are and if they plan to move them.
It insists the government disarms the Janjaweed, as it has promised in the past.
The agreement also obliges all sides to release anyone detained in relation to the conflict, as long as they have not already been convicted of a crime.