(Adds quotes, numbers of troops remaining, SUNA reports full pullout)

By Skye Wheeler

JUBA, Sudan, Jan 9 (Reuters) - Sudan said on Wednesday it had pulled all troops out of the country's semi-autonomous south, while a southern official said roughly 1,000 remained but were expected to trickle north over the next two days.

"The armed forces completed a final 100 percent redeployment to north of the 1956 border in accordance with the Comprehensive Peace Agreement," state news agency SUNA said, referring to the north-south boundary line at Sudan's independence.

Major General James Hoth of the southern army said roughly 1,000 northern troops remained south of the boundary line, but he expected them to leave shortly.

"Almost 90 percent of the soldiers have gone," Hoth told Reuters. "Some, due to transport problems, will return (to the north) tomorrow or the next day."

The redeployment of thousands of northern troops is part of a 2005 peace deal that ended more than two decades of north-south Sudanese civil war, which is separate from the ongoing conflict in the western Darfur region.

Two million people died and about 4 million were displaced in the north-south conflict, fought over ethnicity and ideology and fuelled by oil.

Northern troops had initially been slated to leave the south by July 9, 2007, and hand control of southern oil fields to joint patrols, but Khartoum missed that deadline.

In October, southern ministers walked out of a national coalition government saying Khartoum was failing to implement measures of the peace deal.

The current troop movement appeared aimed to come close to meeting the latest Jan. 9 deadline for withdrawal, after two subsequent deadlines in December set after crisis talks were missed. The new deadline is also the third anniversary of the north-south peace deal.

'HISTORIC EVENT'

Sudan's state news agency quoted Defence Minister Lt-Gen Abdel-Rahim Mohamed Hussein as calling the redeployment an "historic event" and saying he was confident in the will of both sides to implement the peace agreement fully.

SUNA also quoted Hussein as criticising the former southern rebels for not closing two military camps, which he said posed a security threat.

Hoth, speaking to Reuters on a satellite telephone from the oil-rich Unity State, said barracks there had been handed over to special joint units of northern and southern soldiers on Wednesday. These are to patrol oil areas under the peace deal.

Hoth said he believed there were roughly 1,000 northern soldiers remaining across south Sudan, including "about 100" left in Unity State, near the north-south border area.

"There are still remnants," he said. "It is a process. ... All will go in maybe one or two days."

South Sudanese President Salva Kiir had said late last year that 17,000 northern troops remained in south Sudan, mostly in Unity state. Northern officials put the number at 3,600.

Southern officials have accused northern forces of remaining in southern oil areas to retain control of Sudan's main export.

Hoth said that a joint north-south defence board had agreed that the northern soldiers should redeploy to about 10 to 20 km (6-12 miles) above the north-south line, but they had so far not done so.

"They are not going very far. They are just going to the border area," he said. "But maybe they will proceed (further). In a few days we will know." (Writing by Skye Wheeler; Editing by Cynthia Johnston and Caroline Drees)

AlertNet news is provided by