UNITED NATIONS—The remaining 8% of Syria's chemical weapons stock is trapped on a government air base near Damascus behind rebel-held roads, preventing international inspectors charged with eliminating the chemical weapons from reaching it, a top U.N. official said Thursday.

The chemicals are the precursors needed to make sarin gas, and airlifting them from the base has been ruled out as too dangerous, said Sigrid Kaag, who is running the joint U.N./Organization for the Prohibition of Chemical Weapons operation.

Syria faces a June 30 deadline to completely remove its declared chemical weapons stock from the country under a deal brokered by the U.S. and Russia in September. The agreement pulled the U.S. back from the brink of a military strikes on Syria after hundreds of people were killed in a chemical weapons attack outside Damascus in August.

The deadline has been pushed back several times, but in an interview Ms. Kaag didn't blame the Syrian government for stalling, saying the process was highly complex.

She told the Security Council on Thursday that governments with influence over the rebel group blocking the operation should urge the rebels to allow unhindered passage to the air base.