Joseph Kony, leader of the Lord's Resistance Army, held a private meeting with the Ugandan official and Riek Machar, the vice-president of the autonomous government of Southern Sudan in a tent on the Sudan-Congo border.
The LRA has been fighting the Ugandan government in the north of the country since 1989. It says it wants a government based on the biblical ten commandments.
A senior LRA official said: "Kony assured the international community that he is committed to peace and that he is determined to reach an agreement once and for all."
Mediators regard the appearance of Kony as a step forward for negotiations, which began in south Sudan's capital Juba on July 14.
At least 80 LRA fighters formed a cordon around the meeting.
On Monday, Kony met a delegation of 160 officials and politicians from northern and eastern Uganda and representatives of non-governmental organisations.
The meetings were held in a makeshift camp set up for the talks about 3km inside the Congolese border. The camp was decorated in palm leaves as a sign of peace.
"For meaningful talks to continue there must be a cessation of hostilities," the Lord's Resistance Army said in a statement after Monday's talks.
More than 1.5 million people have
been displaced by the conflict
Kony has yet to meet the main Ugandan government delegation, led by Ruhakana Rugunda, the interior affairs minister.
The LRA has been accused of widespread human rights violations including mutilation, torture, rape and carrying out several massacres. More than 20,000 children are believed to have been abducted to serve as soldiers or sex slaves.
More than 1.5 million people in Uganda's Gulu and Kitgum districts have been displaced by the fighting and are living in temporary camps, protected by the army.
The International Criminal Court issued an arrest warrant for Kony in 2005 for crimes against humanity and war crimes.
Kony claims to be a spirit medium; abductees who have escaped from the LRA say he told them he was guided by the "Holy Spirit" and would preach in tongues.
The Lord's Resistance Army is made up of the remnants of a rebellion that began when Yoweri Museveni became president in 1986. The Acholi people of northern Uganda lost much of their influence with the defeat of Tito Okello, the Acholi president, leading to widespread resentment of the government.