The Amarnath cave shrine is considered to be one of the holiest shrines in Hinduism and hundreds of thousands of devotees make an annual pilgrimage to it across challenging mountainous terrain.
His trip to the holy cave comes on the second day of his visit to Ladakh and Jammu and Kashmir.
On Friday, Defence Minister Rajnath Singh reviewed the overall security scenario in Jammu and Kashmir with the top military brass, officials said.
He asked the armed forces to give a fitting reply to any “misadventure” by Pakistan.
At a high-level meeting, the Defence Minister had also asked the armed forces to maintain a strict vigil along the Line of Control (LoC) with Pakistan.