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By Tim Cocks

KAMPALA, May 3 (Reuters) - Uganda's government and the Lord's Resistance Army (LRA) rebels have signed a second phase of their peace deal, but obstacles still remain before the often bogged down process is concluded.

"We signed agenda item number two last night," government spokesman Barigye Ba-Hoku said by telephone on Thursday.

Peace talks between the two sides started in south Sudan last July and produced a truce in August, raising hopes of an end to a conflict that has killed tens of thousands and displaced 1.7 million in northern Uganda.

But the talks have made little progress since, and the LRA has frequently walked out of negotiations.

Ba-Hoku said that although the signing was a significant breakthrough, there was still a long way to go.

"These are the backbone for the agreement," he said. "(But) we've concluded only two agenda items in nine months. We still have three left before a deal, which could take time."

The LRA were not immediately available for comment.

Ba-Hoku said both sides would now break off until Friday 11 May while they consult on phase three of the deal.

Analysts say this document -- concerned with the thorny question of accountability for war crimes -- will be the biggest sticking point.

Phase two of the deal seeks lasting political solutions to the humanitarian catastrophe the war created, including helping refugees go home.

It also tries to address some of the grievances of northerners that helped fuel one of Africa's longest wars.

Talks have frequently stalled, most recently in January, when the rebels walked out, citing security fears. In March the new U.N. envoy for Uganda's conflict, former Mozambique President Joaquim Chissano, met and reasssured LRA leader Joseph Kony near his eastern Congolese jungle hideout.

Kony and four other commanders are wanted in the International Criminal Court over allegations of killing civilians, rape and child abduction.

The rebels have repeatedly said they will never make peace unless the Hague-based court drops the indictments, something the government says it can attempt only after the signing of a final agreement.

The LRA are notorious for beating civilians to death, hacking lips off survivors and abducting children.

The miserable conditions in northern Uganda's refugee camps led the U.N. to describe it as one of the world's worst humanitarian catastrophes.

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