Ugandan President Yoweri Museveni issued the order as a weekend "cessation of hostilities" accord came into force at 6am (1300 AEST) under which LRA fighters will move to camps in southern Sudan for the duration of the talks.
Officials in Kampala said the Ugandan People's Defence Forces (UPDF) were preparing routes of safe passage for the rebels to move to the two sites and would soon begin publicising their locations by radio.
"The commander in chief of the UPDF... has directed all UPDF to cease all search and destroy operations against the LRA," army spokesman Felix Kulaije said, reading from the presidential order.
"It is hereby directed that the UPDF should withdraw to their barracks and to the guarding of internally displaced people," he said. "They should not shoot at the LRA unless in defence of the population."
Peace talks
In the southern Sudanese capital of Juba, where the peace talks are being held, LRA officials said rebel leader, Joseph Kony, who declared a unilateral ceasefire on August 4, had re-affirmed the earlier truce.
"We have just heard that the president has announced a cessation of hostilities (and) that is sufficient to move the process forward," rebel spokesman Obonyo Olweny said.
Uganda's deputy Defence Minister Ruth Nankabirwa said military experts were mapping out safe corridors for the LRA to use to move to the camps.
"We expect the LRA to start using those corridors that will be announced later in the day and our troops have been directed not to shoot at them unless it is to protect civilians," she told a Kampala news conference.
Under the agreement, Uganda has guaranteed the rebels - who number anywhere between 500 and 5,000, according to various estimates - safe passage to the assembly points.
They will stay there under the protection of the government of autonomous southern Sudan, which is mediating in the negotiations that are to resume on Thursday.
The Juba talks are seen by many as the best chance to end northern Uganda's conflict, which has claimed tens of thousands of lives and displaced nearly two million people since the LRA took leadership of a regional rebellion in 1988.
However, mediators have warned of a tough road ahead with the two sides at deep odds on a variety of wealth and power-sharing issues.