By Patrick Nduwimana

BUJUMBURA, May 16 (Reuters) - Senior officials of Burundi's last holdout rebel group returned to the capital Bujumbura on Friday to begin implementing a delayed peace agreement, but the group's leader stayed behind in exile in Tanzania.

A delegation of leaders of the Forces for National Liberation (FNL) landed at Bujumbura's international airport, where they were greeted by diplomats from the African Union and United Nations among others.

Leader Agathon Rwasa remained behind in Tanzania, which has for years led peace efforts in its tiny neighbour. FNL officials declined to say why Rwasa did not come.

"We hope he will join us soon," said the leader of the FNL delegation, Pasteur Habimana. "We thank God that we are back in Burundi. We have come to sort out all the obstacles to implementing the peace deal."

Burundi's government and the FNL signed a pact 19 months ago to bring the rebels, thought to number less than 3,000, out of the bush. But the rebels pulled out of a truce monitoring team, after objecting to some parts of the agreement and saying they feared arrest upon returning home. A 2005 truce fell apart in days.

"This is a big day for Burundi and we hope it will help us complete the programme we have started," said Kingsley Mamabolo, ambassador of South Africa, which is leading the mediation. The FNL's sporadic battles with Burundi's army in the hills around Bujumbura were seen as the last barrier to peace in a nation emerging from more than a decade of war pitting the Hutu ethnic majority against the politically dominant Tutsi minority.

Skirmishes over the last month have killed at least 100 people and displaced thousands in the coffee-growing nation of 8 million on the shores of Lake Tanganyika.

The FNL, a Hutu rebel group, did not take part in the peace process that produced the current government of President Pierre Nkurunziza, himself a former guerrilla from another Hutu group who was elected head of state by legislators in August 2005.

His ascendancy was the final step of a United Nations and African Union-backed peace plan which brought all of Burundi's warring parties save the FNL into a democratically elected coalition government.

The deal was seen as one of Africa's homegrown success stories, since it was spearheaded by regional presidents.

South African troops accompanied the FNL delegation on Friday, and the road from the airport to the city was sealed to protect the delegation.

Despite criticism over corruption and heavy-handed rights abuses, Nkurunziza's government is generally viewed as working towards improving Burundi's moribund economy and integrating thousands of former fighters into its security forces. (For full Reuters Africa coverage and to have your say on the top issues, visit: http://africa.reuters.com/ ) (Writing by Bryson Hull; Editing by Catherine Evans)

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