Sudan and South Sudan have agreed to resume direct flights between their capital cities nearly five months after they were halted during a dispute over the status of South Sudanese living in the north, both sides said on Sunday.

The two countries have been at loggerheads over a variety of issues since South Sudan split away from Sudan a year ago under a 2005 peace deal that ended decades of civil war.

Hundreds of thousands of southerners still live in Sudan, where many have faced an uncertain legal status since an April deadline passed for them to get work and residency documents or be treated like foreigners.

Sudan halted flights between Juba and Khartoum after the deadline because they were no longer domestic and therefore required an international agreement, said Rahamatalla Mohamed Osman, Sudan's undersecretary of foreign affairs.

At the time most South Sudanese living in the north had not been issued passports yet. Juba's embassy in Khartoum has recently started handing out travel documents.

Tickets via Kenya or Ethiopia cost up to four times what Sudanese carriers charged until the suspension, making it hard for many travelers to afford flights.

On Friday, the two civil aviation authorities reached a provisional deal that opens the way for Sudanese carriers to restart direct flights, Osman said by phone after visiting Juba.

"The two countries agreed to resume the flights between the two capitals," he said. South Sudan's transport ministry confirmed the agreement.

So far, Sudan Airways and Marsland have applied, but more airlines will be able to join, he said, adding that the two civil aviation authorities will decide the timing of the first flight.

"We signed the day before yesterday and then the procedures will take place," he said. "I hope it will be soon."

David Martin, undersecretary in South Sudan's ministry of transport, said it was up to Sudan when flights could resume. "We leave it to them. For us we don't have an airline."

South Sudan seceded from Sudan after voting overwhelmingly to secede in a 2011 referendum.

The plebiscite was promised in the 2005 peace deal that ended decades of civil war in which some 2 million people are estimated to have died.