"We condemn the attack on the pilgrims and pray that the departed souls rest in peace. It is an act of cowardice to attack innocent and unarmed pilgrims," he told PTI.
It showed the utter frustration of the terrorists and the "countries supporting them", Fadnavis said, adding that India would give a "befitting reply" to these "criminals of humanity".
The chief minister said he stood in support of the bereaved families, who lost their near and dear ones in the terrorists' gunfire, and prayed for the speedy recovery of the injured.
In a series of tweets, Fadnavis said his government was making arrangements to bring their bodies back.
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He added that the government was in touch with the Centre and the authorities in Jammu and Kashmir.
"Maharashtra Govt has made arrangements for helicopter to bring back the mortal remains of 2 #AmarnathPilgrims to Dahanu from Surat (sic)," he wrote on the microblogging website.
The bodies of those killed in the terror attack were flown to Surat in an Indian Air Force (IAF) plane.