During his visit, Ban is also seeking to bolster a 2005 peace deal that ended two decades of civil war in Sudan but whose increasing fragility could herald the break-up of Africa's largest nation.
The Comprehensive Peace Agreement was signed in January 2005 to end 21 years of war between the Muslim north and Christian and animist south that killed at least two million people and displaced millions more.
"It is crucially important that we implement the CPA ... it is important that the leaders of both the north and the south be fully committed," Ban said in Juba.
A senior UN official travelling with Ban said there were "worrying signals" about the implementation of the peace deal, including delays in the promised pullout of government troops from the south.
The UN official said: "There are a number of signs that show there is a need to push the CPA forward.
"Both sides have indicated their commitment to the agreement but it is important not to let it slip."
In Juba, Ban held talks with Salva Kiir, Sudan's vice-president and a former rebel leader who took over as head of the Sudan People's Liberation Army in July 2005.
While in Darfur, he will visit a camp at Al-Fasher for a first-hand look at the situation before returning to Khartoum on Thursday.
Ban is then scheduled to travel to Sudan's neighbours Chad and Libya.
The UN secretary-general said he had urged Omar Hassan al-Bashir, Sudan's president, to help in the planned deployment of peacekeepers and that al-Bashir had replied that his government would provide "all necessary administrative and logistical support".
Ban said: "Time is of the essence. The government's co-operation is essential on a range of practical matters."
In a separate development, Ban announced he has appointed Ashraf Qazi, currently UN envoy to Iraq, as his new special representative for Sudan. Qazi replaces Jan Pronk.
Ban cited Qazi's "wide and extensive diplomatic experience" in naming him to the post after Pronk was expelled in October 2006 for criticising the army over its conduct against Sudanese rebels.