The security personnel fired teargas shells to disperse the protesters at Habak Crossing. "The situation is under control now," police said.
The were no reports of any injuries. The 21-km half marathon was flagged off in the morning from the Kashmir University at Hazratbal. It was to pass through the banks of Dal Lake along Foreshore Road.
Former Jammu and Kashmir Chief Minister Omar Abdullah was also scheduled to take part in the event. He later cancelled his participation owing to the situation.
As many as 15 international athletes had confirmed their participation in the event for which more than 15,000 people had registered.

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