Sudan's government has missed a deadline to withdraw all its troops from southern Sudan as called for by a landmark peace deal. As Nick Wadhams reports from our East Africa bureau in Nairobi, the news could be a bad omen for lasting peace between Sudan's government and southern rebels.

Under the agreement that ended Africa's longest conflict, Sudan was required to withdraw all its troops from the south by July 9. But a United Nations statement says the north has withdrawn about 66 percent of its troops, leaving more than 15,000 troops where they should not be.

Sudan Liberation Army (SLA) soldier (file photo)

The southern government also alleges that the north has not disarmed or integrated militias that it backed during its 21-year civil war with the Sudan People's Liberation Army. More than 1.5 million people died in the war.

A spokesman for Sudan's Foreign Ministry, Ali Sadiq Ali, insists that the government in Khartoum continues to uphold the spirit of the Comprehensive Peace Agreement and will withdraw its troops.

"There are some delays here and there, not only the withdrawal of troops, there are delays in so many areas, some areas have been fulfilled to the book," he said. "The political will is there. I am very optimistic. I don't think the delays are intentional or they reflect bad faith from either side. I am sure that the government of Sudan will abide by the agreement."

The news that government troops remain in south Sudan could cause trouble because the southern government is supposed to take over security on Tuesday. The 2005 peace deal created an autonomous government in the south and was supposed to establish two separate armies.

The south is also home to massive oil reserves, where the two sides were supposed to deploy joint units. There are some fears that the north's troops have stayed behind in oil-rich areas. Sadiq denied those reports.

The peace deal has managed to hold so far despite violations by both sides. In 2006, the southern forces ignored a deadline that required them to withdraw from areas of eastern Sudan.

And 150 people were reported killed in the town of Malakal in fighting between the north and the south. Those clashes were sparked by northern-backed militias and were the most serious violation of the peace accord since it was signed.

The civil war was fought between the largely Christian Sudan People's Liberation Army in the South and the forces of the Sudanese government in the north, which is mostly Muslim.

The war and the peace deal are entirely separate from the ongoing conflict in Darfur, in Sudan's west.