Pagan Amum, South Sudan's chief negotiator, told reporters both Sudan and its neigbouring country South Sudan were trying to see "how can we remove the obstacles to implementation of the cooperation agreements, to the benefit of the two nations" and improved security for both.
He spoke following talks with Nafie Ali Nafie, assistant to President Omar al-Bashir. After arriving on Saturday, Amum met with Sudanese negotiators as well as Defence Minister Abdelrahim Mohammed Hussein.
Concern has grown that the September agreements have not taken effect after Bashir and his South Sudanese counterpart Salva Kiir hailed them as ending conflict.
The two countries fought along their undemarcated border in March and April, and tensions flared anew late last month when South Sudan blamed Khartoum for aerial bombing which it said killed seven civilians.
Mediated by the African Union, the deals included setting up a demilitarised border buffer zone to cut support for insurgents in Sudan and to allow a resumption of South Sudanese oil through northern pipelines for export.
In January, South Sudan halted crude production -- which accounts for almost all of its government revenue -- after accusing Khartoum of theft in a long-running dispute over transit fees.
The security arrangements have to fall into place before oil can flow and the borders open again to trade, Princeton Lyman, the United States special envoy to Sudan and South Sudan, said on Thursday after talks with officials in Khartoum.
He said a lack of trust between Khartoum and Juba has prevented implementation of the deals, and warned that obtaining that trust will be difficult unless an insurgency ends in Sudan's border states of South Kordofan and Blue Nile.
Sudan has accused South Sudan of supporting the south's former civil war allies in the rebel Sudan People's Liberation Movement-North (SPLM-N).
Analysts believe the charge, despite denials by Juba which in turn accuses Khartoum of backing rebels on southern territory.
The deal on demilitarisation came in the context of each side agreeing not to support armed rebels in the other country, Lyman said.
Separately from Amum's visit, a political and security dialogue between officials from Sudan and South Sudan is expected to take place in Khartoum this week in a further effort to resolve differences.
The September deals did not include agreement on another crucial issue, the future of the flashpoint Abyei region. The African Union set a deadline of December 5 for the two countries to settle Abyei's final status or be bound by an AU proposal for a referendum in October next year.
South Sudan separated in 2011 under a peace agreement that ended 23 years of civil war.