"Our doors are open for whoever wants and seeks peace, and for whoever does not rely on foreign powers and brutal agendas," al-Bashir was quoted as saying by the SUNA news agency.
He specifically called on the Justice and Equality Movement (JEM) to "join the peace process and to take the side of dialogue for the sake of peace", DPA reported
JEM's leader, Khalil Ibrahim, was killed in December by the Sudanese military, reportedly while trying to cross into South Sudan.
Ibrahim reportedly returned to Sudan from Libya this year, after the downfall of Moamer Gaddafi's regime, from whom JEM allegedly received support. Khartoum also accuses newly independent South Sudan of aiding the rebels.
The group, along with other key rebel movements in the western region, pulled out of a peace deal brokered last year by Qatar. Some smaller rebel movements have stuck with the agreement.
The conflict in Darfur, ongoing since 2003, has claimed some 300,000 lives according to the UN, although Khartoum says the figure is lower.