Medecins Sans Frontieres (MSF) has pulled out of some conflict-hit parts of Sudan due to a lack of cooperation from authorities, the medical charity said on Thursday, as the country suffers increasing violence.

Sudan has faced a rebellion in Darfur since 2003 and a separate but linked insurgency in Blue Nile and South Kordofan since the secession of South Sudan in 2011.

The group said that total denial of access to Blue Nile, forced closure of activities in East Darfur and administrative obstacles in South Darfur had made its work in those areas impossible, accusations that Sudan has denied.

"Our experience is that the Sudanese government arranges meetings specifically to prevent international aid, rather than to facilitate it," Bart Jassens, the director of operations for MSF in Brussels, said in a statement.

Violence has increased in Darfur since the government asked the UN-African Union peacekeeping mission to leave in November, and in Blue Nile and South Kordofan since ceasefire talks collapsed in December.

The organization has ceased operations in East and South Darfur, and will no longer request permission to work in Blue Nile after all of its requests were denied, spokeswoman Beatrice Debut said from Nairobi.

The regions where operations have been halted were run by a Brussels-based section of MSF. The group's activities in North and West Darfur, which are run by other sections of MSF, would continue, while operations in South Kordodan remain suspended since an MSF hospital was bombed there last week, Debut said.

The Sudanese government denied that it had blocked MSF's work in Darfur, saying that it had never received requests to work in Blue Nile and that the Belgium-based section of MSF had filed paperwork to leave the country in September.

"This organization had not faced any systematic obstacles to their work in Sudan," Mohammed Fadlallah, Sudan's acting commissioner of humanitarian affairs, told Reuters.

"As for the hospital in South Kordofan, this is a mixing of subjects because that is run by the French MSF, which is not registered in Sudan and is working in areas under the control of the insurgency, which is unacceptable and illegal," he said.