Jan Egeland had hoped to secure humanitarian gestures from rebel leader Joseph Kony as a way to boost talks aimed at ending the 20-year-long conflict in northern Uganda that has killed tens of thousands.
Egeland wanted the rebel leader to release women and children the LRA may be holding and to allow any wounded captives go to hospital.
The LRA wants the International Criminal Court to revoke arrest warrants against Kony and other leaders.
During a 10-minute meeting in a green UN tent, Kony's first with an international official of Egeland's rank, voices were raised and the discussion was heated.
Kony said afterwards no deal was reached.
"We don't have any children. We only have combatants. There are no wounded," said the rebel leader in a rare statement to the media.
This month the Ugandan government and the LRA signed an extension of a truce during talks in Juba, capital of southern Sudan, but the discussions have been slow and marred by mistrust on both sides.
The ICC in Netherlands has issued arrest warrants for Kony and other LRA leaders for crimes against humanity after human rights groups accused the rebels of enslaving children and mutilating their victims.
Vincent Otti, the LRA deputy leader, said the question of the warrants came up in the talks as an obstacle to Kony and his lieutenants taking part in negotiations with government.
"If the warrants are lifted, then we can go to the peace talks," Otti said.
LRA officials had said it was unlikely Kony would agree to Egeland's request that he release women and children.
"These people are families. They don't want to leave," said one.
Kony, a self-proclaimed mystic, wants to rule Uganda by the Biblical Ten Commandments and is opposed to the government of Yoweri Museveni.