The students of Gandhi College boycotted their classes and came out on the main road at Babademb in downtown city around noon and tried to take out a march, officials said.
They were chanting slogans in support of the demand for release of those arrested during such protests earlier, the officials said.
When they were prevented from marching further, the students pelted stones at the police.
There was no immediate report of any casualty in the clashes which were continuing when last reports were received, they said.
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The officials said a large group of students also staged a demonstration at Hajin chowk in Bandipora district of north Kashmir.
The protest ended peacefully, they said.
Kashmir has been witnessing random protests by students at various places since April 15 when police raided a college in Pulwama district of south Kashmir.
Students of Sri Pratap Higher Secondary School in Srinagar have been indulging in protests repeatedly because of which studies were suspended for several days last month.
Concerned over the continuing agitation by students, Jammu and Kashmir Governor N N Vohra held a series of meetings with Education Minister Altaf Bukhari and vice chancellors of Kashmir based universities and education department administrators last week to review adherence to educational schedules and protection of students from involvement in law and order incidents.
Bukhari, on his part, also held a number of meetings and urged legislators and the civil society to take ownership of the educational institutions in their respective areas to transform these as vibrant hubs of learning.
"We will work with dedication to make the department an example and the results will be seen on ground within three months," Bukhari had said chairing a meeting here yesterday.
He had said he would visit every constituency personally to know about the needs and issues in different schools.
"School children are our future and we have to promise them best education and for that we need to reach out to them," he said.