Almost 1,000 South Sudanese left their squalid camp in the Sudanese capital to return home on Tuesday but there is little immediate hope for about 40,000 others who remain, officials say.
South Sudan's embassy and the Africa Inland Church arranged the convoy to Malakal, in South Sudan's Upper Nile state, after Sudanese authorities asked them to leave their camp around the Shajara train station in south Khartoum, said Kau Nak, the embassy's deputy head of mission.
"Some of them are still loading" and the last of the vehicles will leave by Wednesday, he told AFP.
Many South Sudanese have been waiting in camps like Shajara around the Khartoum area for more than two years, since before South Sudan became independent in July 2011.
At last count there were more than 100,000 Southerners left in the Khartoum area alone, according to Nak.
"All of them are waiting for means of transport. All of them lost their jobs. All of them lost their nationalities, and nobody's supporting them," he said.
Insecurity and lack of resources have hampered efforts by aid agencies to transport the southerners, the United Nations Office for the Coordination of Humanitarian Affairs (OCHA) said on its website.