The soldiers, who set up camp in a base 10 kilometres (six miles) southeast of Khartoum, are all from the Sudan People’s Liberation Movement (SPLM) that fought a bloody 21-year civil war against the regime.
They were greeted by Sudanese intelligence chief Mohammed Hassan Fadel and will soon establish the first Joint Integrated Unit (JIU) with an equal number of northern government troops, an AFP correspondent reported.
Under the accord Khartoum and the SPLM signed on January 9 in the Kenyan capital Nairobi, joint units are to be formed to ensure compliance with the permanent ceasefire.
The JIUs, comprising nearly 40,000 soldiers are to be deployed in areas that were affected by the north-south conflict, including south Sudan, the Nuba Mountains and southern Blue Nile, as well as Khartoum.
The accord called for the deployment of a 24,000-strong integrated unit in south Sudan, 12,000 split equally between southern Blue Nile and the Nuba Mountains and a 3,000-strong JIU to be based in Khartoum.
It also set a two and a half year deadline starting from the peace agreement’s signing date for the government to pull out its forces from the southern region and a year for the SPLA to redeploy from the north.
Both should have started withdrawing immediately after the January 9 peace deal but have fallen behind schedule.
The peace accord provides for a referendum by southern voters after a six-year interim period.
"If the result of the referendum is in favor of secession of the South from the North, the JIUs shall dissolve... to pave the way for the formation of separate Armed Forces for the emerging states," the agreement stated.
These units "shall form the nucleus of the future Sudanese National Armed Forces (SNAF) should the result of the referendum... confirm unity of the country," it added.
The SPLA is the military branch of the Sudan People’s Liberation Movement that signed the peace agreement with Khartoum.
First Vice President Salva Kiir now heads the SPLM following the death of historical southern leader John Garang in a July 30 helicopter crash.