(Add Sudanese government move against SPLM in north)
By Hereward Holland
JUBA, Sept 3 (Reuters) - Seventeen people were killed in fighting between Sudan's army and rebels aligned to South Sudan in a Sudanese state on the border with the newly independent south, the official news agency SUNA said on Saturday.
Up to 3,000 people fled armed clashes in the region, the United Nations refugee agency (UNHCR) reported, calling for an immediate halt to fighting to prevent a humanitarian crisis.
Analysts say Sudan's government in Khartoum is trying to strike against the rebels in South Kordofan and Blue Nile states before they become a serious political and military threat. The fighting risks drawing South Sudan into a proxy war.
The Sudanese government has accused the south's dominant Sudan People's Liberation Movement (SPLM) of being behind the violence in Blue Nile and South Kordofan. The SPLM-North, the movement's branch in Sudan, has blamed Khartoum.
Ali Abdel-Latif, an SPLM-North official, told Reuters that Khartoum security officials informed the group the government was banning its activities in Sudan. "They asked us not to practice any political work in the name of the SPLM," he said.
He said security forces had also taken control of SPLM-North's main offices in Khartoum.
There was no immediate official comment from Khartoum.
SUNA said 17 people were killed and 14 wounded in the fighting in South Kordofan, but gave no further details.
South Sudan seceded from Sudan -- at the time Africa's largest country -- six years after a ceasefire that ended decades of civil war between north and south. South Sudan denies Khartoum's accusations that it is supporting the rebels.
SPLM-North battled alongside the South in the civil war but its areas of influence remained north of the border after separation in July. The oil-producing south voted to split from the north in a January referendum promised in a 2005 peace deal, the Comprehensive Peace Agreement (CPA).
"Both the ruling National Congress Party and the SPLM-North are signatories (to the peace deal) so we don't expect them to turn to armed hostilities," South Sudan's information minister, Barnaba Marial Benjamin, told Reuters.
"We urge them to go back to the CPA and the popular consultations for resolving the issue."
Sudan's information minister, Kamal Mohamed Obeid, said South Sudan was involved in the violence.
During the popular consultations people from Blue Nile overwhelmingly asked for autonomy from Khartoum. The consultations were never held in Southern Kordofan.
Qamar Dalman, an official with the South Kordofan branch of the SPLM, told Reuters that about 14 government soldiers were killed during the clashes in South Kordofan.
"All the civilians had fled the area and the ones who were killed were from the government, not civilians," Dalman told Reuters by telephone.
In Blue Nile, clashes and Sudanese air strikes on Friday forced many people to flee, UNHCR spokesman Peter de Clerq said.
"Between 2,500 and 3,000 people crossed into Ethiopia yesterday morning but the number will have gone up since then," he said.
"In (the town of) al-Damazin there was serious fighting yesterday but we're not sure how many people have left. We understand that significant numbers of people are trying to leave al-Damazin."
UNHCR chief Ant?nio Guterres appealed for an immediate halt to the hostilities amid reports of escalating displacement.
"We need, at all costs, to stop yet one more refugee crisis in a region of the world that has been witnessing in recent months so much suffering," said Guterres in a statement after visiting conflict and famine-ridden Somalia.
Yasir Arman, secretary-general of the SPLM's northern branch, said eight people had been killed in al-Damazin including two women, a child and four SPLM-N members.
"Many SPLM-North were arrested in al-Damazin and we're not sure of their fate. We're worried because all those who were arrested in South Kordofan were slaughtered by security agents," he said.
Last week international rights groups said witnesses saw Sudanese government soldiers and militia shoot people in the streets and carry out both house-to-house searches and stops at checkpoints using lists of names of SPLM supporters in the South Kordofan state capital Kadugli and other areas.
Some analysts believe the SPLM-North is now politically isolated and needs partners in order to sustain its rebellion.
"(The SPLM-North) are now a rebel group. The only way for them to survive is through insurgency and rebellion until they can negotiate a political settlement," Fouad Hikmat of the International Crisis Group told Reuters.
"They need to sustain this rebellion and therefore need partners in the neighbourhood -- South Sudan and Ethiopia."
The Sudan government declared a state of emergency in Blue Nile state on Friday and said it was replacing elected governor Malik Agar, who is a member of SPLM-North, with a military ruler, SUNA said. (Additional reporting by Khalid Abdelaziz in Khartoum; Writing by Amena Bakr and Edmund Blair in Cairo; Editing by Karolina Tagaris)