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(Adds reaction of two other rebel groups in final two paragraphs)
By Lin Noueihed
DUBAI, Feb 17 (Reuters) - Sudan's government and a leading Darfur rebel faction agreed on Tuesday to meet for peace talks, signing a deal with concessions from both sides, and the Qatari mediator urged all other rebels and Chad to come to the table.
Tuesday's agreement included measures to aid and protect refugees in Darfur and a commitment by the two sides to continue negotiations in Doha. The Justice and Equality Movement (JEM) also wants a prisoner swap.
JEM said it would release some of its Sudanese government detainees as a show of goodwill. The prisoner issue is a thorny one that has come close to frustrating Qatari efforts.
Sudan started negotiations last week with JEM, almost six years into a conflict that international experts say has killed 200,000 people and uprooted 2.7 million.
But other influential rebel factions are refusing to talk to Khartoum and the cooperation of neighbouring Chad, which hosts refugees fleeing Darfur, is seen as key to any lasting peace.
"I want to clarify that this agreement is open to all the other factions," Qatari Prime Minister Sheikh Hamad bin Jassim al-Thani told reporters in Doha, where the talks are being held.
"This process should also involve an agreement between Chad and Sudan as this will help a great deal to resolve the issue. We and the brothers in Libya are trying and hope very soon to be able to do something as this will ... make it not just a peace among Sudanese but also with its neighbours."
The preliminary agreement comes as Sudan awaits a ruling from International Criminal Court judges within weeks on whether to issue a warrant for President Omar al-Bashir's arrest over allegations that he was behind genocide in Darfur.
JEM and other Darfur rebels took up arms against the government in 2003, demanding better representation and infrastructure for the Western region.
Khartoum mobilised mostly Arab militias to crush the revolt but denies U.S. accusations this amounted to genocide.
JEM, which also demands Khartoum pledge not to impede humanitarian aid and refrain from harassing displaced people, has said it supports Bashir's indictment. But the group's leader Khalil Ibrahim said it was committed to pursuing peace talks.
At least 50 alleged JEM members are imprisoned in Khartoum, after being sentenced to death on charges of taking part in JEM's unprecedented May attack on the capital.
They include Ibrahim's half brother Abdel Aziz el-Nur Ashr.
"The movement wants all the parties to the dispute to take part in these negotiations," Ibrahim said, adding that his group was negotiating on behalf of all Sudanese not just JEM.
"Hopefully, we will have the goodwill to reach a just and comprehensive deal that will end Sudan's problems in Darfur."
But other rebel factions were quick to dismiss Tuesday's agreement as destined to failure.
"Any comprehensive peace agreement in Darfur should bring in everybody -- small factions and big movements. This communique will do nothing to bring about a general peace," said Abdelaziz Sam, adviser to a branch of the Sudan Liberation Army (SLA) which signed the failed 2006 Darfur Peace Agreement with Khartoum.
"Both of the parties are only doing this to achieve their own aims ... JEM wants to get its detainees released. And the National Congress Party wants to show it is doing something positive in Darfur to avoid the International Criminal Court."
SLA's Unity faction and the United Resistance Front -- said the accord was meaningless with JEM as the only rebel signatory.
"The people of Darfur have paid dearly and they deserve better than is happening in Doha," said Sherif Harir, a senior Unity member, adding his movement would not take part in talks.