Minor injuries were sustained by both sides, police said.
The strike paralysed life across the state for the second day with shops, markets and business establishments closed and vehicles off the roads.
The general strike has been called by the student wing of Joint Committee on Inner Line Permit (ILP) System demanding implementation of the system to regulate the influx of non-domiciles into the state.
They are also demanding action against police personnel who allegedly committed brutality on student protesters.
The protesters blocked roads to the capital complex by piling metal pipes and placing boulders and felled trees. They also burnt tyres to prevent movement of people and vehicles.
In Manipur's Imphal East district women supporters staged sit-in protests, rallies and formed human chains at Khurai and Wangkhei.
In Imphal West district they held rallies by blocking roads at Uripok, Thangmeiband, Sagolband, Keishampat, Keishamthong, Singjamei and Yaiskul, police said.
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