At least 36 children have died after they received UN-sponsored tainted measles vaccines, according to reports.
Doctors of the clinics in rebel-held towns Jirjanaz and Maaret al-Nouman, in the north-western province of Idlib, said the children started feeling ill shortly after they received the vaccinations.
Parents accused the Syrian opposition - which controls Idlib - of negligence when storing the vaccines and of supplying out-of-date medications.
The Syrian opposition, however, denied the allegations and said the vaccines came from the UN and the World Health Organization (WHO), and could have been contaminated by people close to Syria's President Bashar al-Assad.
"Primary investigations point to a limited security breach by vandals likely connected to the regime, which has been attempting to target the medical sector in Free Syria in order to spread chaos," the opposition health ministry said in a statement.
Bashar Kayal, a health official, told Radio Hawa Smart, "The symptoms don't just indicate spoiled vaccines – it suggests they've been contaminated."
The vaccination programme was stopped immediately after the incident and blood samples have been sent to Turkey for further examinations.
Health minister Adnan Hazouri vowed to resign if an investigation on the children's deaths upheld allegations of negligence.
Monther Khalil, head of the medical department in Idib, reassured the parents of children who have already been injected that they are out of danger.
"The vaccine is completely fine and there is no risk to children who have already been injected.
"We have already vaccinated 60,000 children against measles and there has been no previous problem. The same crews also previously carried out a polio campaign, where they vaccinated 252,000 children across seven rounds, and there were no abnormal complications."
Idlib is held by moderate rebels opposed to Assad and to terror group Islamic State - formerly known as Isis.
The province was subjected to a fierce military campaign in 2014, after which rebels re-gained control of the area.
Last October, the UN announced that "millions of Syrian children" were to be vaccinated against measles, polio, mumps and rubella.
Due to the civil war, at least 200,000 children have not received vaccinations in Syria where, prior to the conflict, the rate of vaccination was of 95%.
Syria's civil war, erupted in 2011, has caused more than 190,000 deaths and 6.5 million displaced people, many of whom are in need of urgent medical care.