BUJUMBURA, May 28 (Reuters) - Burundi troops shot dead two rebels on Wednesday in a clash just two days after both sides declared an end to fighting, the military said.

Fighting between the Forces for National Liberation (FNL) and government troops had killed nearly 100 people in recent weeks. But they agreed on Monday to halt hostilities.

Both sides tried to play down Wednesday's incident.

"It will take time for both sides to respect the truce, but I don't think the incident will stop the peace process," said FNL spokesman Pasteur Habimana. "Everyone needs peace now."

The FNL is the last remaining rebel group from more than a decade of civil war that killed some 300,000 people.

"Our troops told a group of FNL fighters who were coming towards their position to stop, but they refused," said army spokesman Colonel Adolphe Manirakiza.

"So they considered this a provocation and shot at them."

The clash took place in the rebel stronghold of Gihanga, 15 km (9 miles) out of the capital Bujumbura, early on Wednesday.

The return of FNL officials 12 days ago from neighbouring Tanzania has brought hope a delayed peace deal, first signed in September 2006, will finally be implemented.

The FNL conflict is seen as the final hurdle to lasting stability in the coffee-growing nation of 8 million people. (Reporting by Patrick Nduwimana; Editing by Helen Nyambura-Mwaura) (For full Reuters Africa coverage and to have your say on the top issues, visit:http://africa.reuters.com/)

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