The withholding of government aid to trapped civilians in Sri Lanka, Pakistan and Sudan contributed to the worst humanitarian emergencies of 2009, a medical group said today.

Civilians stand behind the barbed-wire perimeter fence of the Manik Farm refugee camp near Vavuniya, Sri Lanka. (Photograph: David Gray / Reuters) Médecins sans Frontières (MSF) also pointed to a fall in funding for the treatment of diseases such as sleeping sickness and HIV/Aids as part of its annual list of worst humanitarian crises for the past year.

"There is no question that civilians are increasingly victimised in conflicts and further cut off from lifesaving assistance, often deliberately," said Christophe Fournier, the MSF international council president. "In places like Sri Lanka and Yemen, where armed conflicts raged in 2009, aid groups were either blocked from accessing those in need or forced out because they too came under fire. This unacceptable dynamic is becoming the norm."

In Sri Lanka, tens of thousands of civilians were trapped with no aid and limited medical care as government forces battled Tamil Tiger rebels in the spring with aid organisations banned from entering the conflict zone. In some conflicts, hospitals themselves came under fire. In what MSF described as a glaring case of abuse of humanitarian action for military gain, civilians who gathered with their children at MSF vaccination sites in North Kivu, in the Democratic Republic of the Congo (DRC) came under attack by government forces.

MSF said its teams were vaccinating thousands of children against measles at seven sites in territory controlled by Hutu militias when the Congolese army opened fire in October, despite security guarantees from all sides. Thousands were forced to flee, and MSF had to evacuate its teams to the regional capital, Goma.

"We feel we were used as bait," said Luis Encinas, head of MSF programmes in Central Africa. "The attack was an unacceptable abuse of humanitarian action to fulfill military objectives." The MSF vaccination campaign continued in other areas and reached a total of 165,000 children.

Elsewhere in Africa, medical humanitarian emergencies persisted throughout 2009 in several parts of Sudan. Besides the crisis in Darfur, people in southern Sudan faced a bleak situation marked by escalating violence, disease, and little or no access to health care. Violent clashes in Jonglei, Upper Nile, Warrap, and Lakes State throughout the year left hundreds dead and thousands displaced. Sporadic attacks on villages by the notorious Ugandan rebel group, the Lord's Resistance Army (LRA), near the Congolese border and also in the DRC itself, caused thousands of Sudanese people to flee their homes and Congolese refugees to cross the border and seek refuge in Western Equatoria state, Sudan.

In Pakistan, where tens of thousands fled a government offensive against the Taliban in the Swat valley, hospitals were struck by mortar fire and two MSF workers were killed forcing the group to suspend its operations.

MSF also highlighted the less reported humanitarian emergencies caused by disease, which claim many more lives than war. It accused donor countries of jeopardising years of success in increasing treatment for people with HIV/Aids because of cuts or limits to funding in international programmes.

"Just when more and more people were accessing crucial medicines and medical experts were acknowledging the need to put people on treatment sooner, patients will be turned away from clinics because the funding just won't be there," Fournier said. "The timing could not be worse."

The neglect also extends to childhood malnutrition, a treatable condition that is the underlying cause of up to half of the annual 10 million preventable deaths of children under five each year.

"International assistance to fight malnutrition amounts to $350m, while the World Bank estimates $11.2bn is required to adequately combat the disease in 36 high burden countries," MSF said. "Additionally, most food assistance is made up of costly and inefficient in-kind donations containing products of poor nutritional value that must be shipped overseas."

Other diseases, such as Chagas, kala-azar, sleeping sickness, and Buruli ulcer continue to be neglected, with very few new commitments to expanding access to available treatment or carrying out research for much needed newer and more effective drugs.