Badri Prasad (25), a resident of Uttar Pradesh, was killed when he was hit by a falling stone from a hillock at Railpathri along Baltal-cave route, they said.
Nand Kishore Lal (66), also a resident of Uttar Pradesh, died of cardiac arrest at Baltal base camp, while body of a sadhu identified as Ram Saroud was found dead near the holy shrine, the officials said.
In another incident, Navratna Devi of Bihar suffered a massive heart attack while crossing Sangam top along the traditional Pahalgam-cave route and died while being shifted to a nearby make shift hospital, the officials said.
Shiv Karam (73), a resident of Madhya Pradesh, died at Baltal base camp hospital, where he was admitted after he had suffered a heart attack.
As many as 4,82,950 pilgrims have visited the cave shrine till last evening, while 10,000 more offered their prayers by late this afternoon.
The annual Amarnath yatra commenced on June 25 from the twin tracks from Baltal and Pahalgam and scheduled to end on August 2, coinciding with the Raksha Bandhan festival.