Obonyo Olweny, the Lord's Resistance Army spokesman, said that Ugandan forces have been massing along the routes.
Olweny said: "These deployments are obstructions to our forces as they move towards assembly areas in southern Sudan."
The government denied the claim, saying it was providing food and communications equipment.
Despite the complaints, talks between both sides continued in the hope of ending one of the most brutal, but least known conflicts in the world.
The insurgents, notorious for cutting off the tongues and lips of civilians and enslaving tens of thousands of children during their two-decade-old insurgency, signed a truce with the government late last month.
The deal calls for Lord's Resistance Army fighters to gather in largely uninhabited areas across the border in southern Sudan, where they will be protected while a broader peace deal is negotiated.
If both sides reach a comprehensive deal, it will be a major breakthrough in pacifying the African region that joins northern Uganda, eastern Congo and southern Sudan.
Insurgents from all three nations operated across the borders with impunity for decades until a peace accord halted Congo's civil war in 2003 and southern Sudanese fighters joined Sudan's government in 2005.
The Lord's Resistance Army was formed from the remnants of a northern Ugandan rebellion that began in 1986 after Yoweri Museveni, the president, overthrew a brutal military junta.
Joseph Kony, leader of the Lord's Resistance Army, mixed northern politics with religious mysticism, declaring himself a Christian prophet fighting to rule the country of 26 million people by the ten commandments.
UN officials estimate that Kony's fighters kidnapped some 20,000 children over the past 19 years, turning the boys into soldiers and the girls into sex slaves for LRA commanders.