Authorities clamped curfew in three towns, including Tral in Kashmir, and imposed restrictions on the movement of people in the rest of the valley.
"The yatra has been been suspended from the Bhagwati Nagar basecamp in Jammu due to law and order situation in the Kashmir Valley," asenior police officer said.
Police and paramilitary personnel were deployed in strength across Kashmir to handle any security challenge.
The number of pilgrims paying obeisance at ice lingum of LordShiva at the 3,880-metre high cave shrine of Amarnath in SouthKashmir himalayas has crossed the one-lakh mark as over 1.15 lakhdevotees had darshan at the shrine.
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A total of 25,294 pilgrims and sadhus have left Jammu for Amarnath in eight batches since the yatra began.
Nine people including a security officer have died in the ongoing Amarnath pilgrimage.
"As many as 1,15,841 pilgrims have had darshan at the caveshrine since the beginning of the yatra," an official spokesman said.
Amid multi-tier security, the 40-day long yatra began from Jammu on June 28 as the first batch of pilgrims left fortwin base-camps of 3,888-metre high cave shrine in south Kashmir Himalayas.
The annual yatra in Kashmir began amid a terror threat, according to an intelligence warning which has prompted the authorities to mobilise the "highest level" of security measures, including satellite tracking system.