According to government spokesman 372,909 pilgrims visited the shrine. Of them, 40 pilgrims died because of ill-health and in accidents.
"This year we have been able to minimize deaths during the pilgrimage and of the dead, four died in cylinder blast and two due to shooting stones," Dr. Saleem -ur- Rehman, a top official of Health department told Xinhua on Tuesday.
The pilgrimage officially culminated on Sunday with the special prayers held at cave shrine located 3,888 meters above the sea level.
"The annual pilgrimage concluded with chanting of religious hymns in the spiritual ambiance of south Kashmir Himalayas," said a government spokesman. "The Governor N N Vohra and top officials of the Hindu shrine board participated in the special pooja ( prayers) at the cave shrine."
Vohra is the chairman of Shri Amarnath Shrine Board (SASB) responsible for conducting the pilgrimage.
Officials had opened two trek routes leading to the shrine -- one from Pahalgam, about 100 km south of Srinagar city (region's summer capital) and another from Baltal around 110 km north from Srinagar.
Even helicopter services were pressed in to fly pilgrims to the shrine. The holy cave houses the ice stalagmite, referred by Hindus as Shiv Lingam (the phallus of Lord Shiva).
The pilgrimage began on June 27.
The region's health department had deployed more than 400 people to provide proper healthcare facilities for the pilgrims in order to bring down the deaths.
"This year we made significant investments in terms of manpower and advanced medical equipment as mandated by the federal ministry of health and as had been desired by the Supreme Court of India," Rehman said.
The health department had set up 10 emergency aid centres, 10 medical aid centres and four base camp hospitals.
"Our centres were equipped with high-tech medical gadgetry including Hyperbaric Chambers (HAPO bags), Defibrillators, Oxygen Concentrators, Automated Chest Compression Systems, Multi- parameter Cardiac Monitors, Pulse Oxymeters," Rehman said. " Besides this the necessary drugs including life saving medicines and diagnostic kits were kept available to save precious lives."
Authorities had also deployed around 300 companies of Police and India's paramilitary Central Reserve Police Force (CRPF) personnel along the routes to thwart militant attacks on pilgrims and ensure hassle free pilgrimage.
Environmental groups accuse board of playing havoc with the fragile environment enroute the cave shrine by increasing flow of pilgrims and increasing the duration of pilgrimage from 15 days to more than two months.
Separatists demanding end of New Delhi's rule in the region too cite environmental concerns and ask government to restrict the annual pilgrimage to 15 days.