Before the 17-month-old revolt against President Bashar al-Assad, Syria produced 90 per cent of its medicines and drugs, but production has been hit by the fighting, lack of raw materials, impact of sanctions and higher fuel costs, the UN agency said.
Ninety per cent of Syria's pharmaceutical plants are located in rural Aleppo, Homs and Damascus provinces and they have suffered substantial damage from the escalation in fighting, WHO spokesman Tarik Jasarevic said.
"Many of these plants have now closed down as a result of the ongoing clashes and increased cost of fuel, resulting in a critical shortage of medicines," he told a UN briefing in Geneva.
Drugs for tuberculosis, hepatitis, hypertension, diabetes and cancer are urgently needed, as well as haemodialysis for kidney diseases, according to the WHO.
Health centres have been closed or damaged or taken over by fighters, while others have been cut off by the violence.
"The health facilities that have stopped functioning are located in the most affected areas where the urgent need for medical and surgical interventions is the most prominent," Mr Jasarevic said.
The Syrian health ministry has reported that it has "lost" 200 ambulances over the last few weeks, he added.
The heightened violence in the conflict has recently spread to Syria's two largest cities, Aleppo and the capital Damascus, exacerbating the humanitarian crisis in the major Arab states.
Fear of the fighting has prompted many citizens to leave their homes. Many banks have run out of cash and the wheat harvest is likely to be wrecked because of the shortage of labour, UN agencies have said.
The UN World Food Programme, which had hoped to provide 850,000 Syrians with food by the end of July, only managed to reach 542,000, WFP spokeswoman Elisabeth Byrs said.
Around 124,000 Syrians have fled across the borders and registered as refugees, while 1.5 million are estimated to be displaced within Syria.