The leader of the ruling National Congress Party (NCP) welcomed the delegation on Sunday, Aljazeera's correspondent in Khartoum Al-Tahir Mardi reported.
The delegates will have talks with government officials and NCP to prepare to implement the peace deal and to draft a transitional constitution.
NCP Secretary-General James Wani, who heads the delegation from south Sudan, is the most senior member of the Sudan People's Liberation Movement (SPLM) to visit Khartoum since the war began in 1983.
Sunday's visit was his first in 21 years to the capital.
Three months of meetings will begin with the aim of writing a new constitution to form the basis of a power-sharing government between Khartoum and the former rebels.
Wani said meetings had begun with leading members of the ruling National Congress Party (NCP), which dominates government and parliament.
Under the January deal, the rebels and the government are to form a coalition government, decentralise power, share oil revenues and form joint military units.
The rebels and the government
will form a coalition government
The SPLM has opened six offices in Khartoum and 11 others throughout the country to register new members as it transforms into a political party from a military movement.
The SPLM team was due to arrive in Khartoum soon after the signing of the deal on 9 January, but arrival was delayed because of logistical problems.
Although this puts the plan to form a new government of unity within six months of the deal under pressure, diplomats said the schedule was ambitious anyway and they expected a delay.
"The timeline was awfully tight and it's not surprising that there's been some slippage as both parties sort out their own structures," one senior Western diplomat said.
Wani told Reuters that the delay was because of other political forces disputing the make-up of the constitutional commission and that he had come to Khartoum to solve these problems.
The composition should be 52% NCP and 28% SPLM, with other northern political forces taking 14%. Southern parties have 6%.
SPLA leader John Garang will be
Sudan's new vice president
"This they believe is too little and this is the main reason they are not satisfied," he said. "We will engage all of them in talks."
He said as soon as the percentages were agreed upon, the commission could start work.
Once a constitution is approved, the new government will be sworn in and SPLM leader John Garang will come to Khartoum to take up the position of first vice president.
Diplomats said this could happen as early as June or July.
Sudan's southern conflict broadly pitted the Islamist government based in Khartoum against mostly Christian or pagan southern rebels, complicated by issues of oil, ethnicity and ideology.
It claimed more than two million lives mostly from hunger and disease and forced at least four million to flee their homes.