"Regardless of my disagreements with the Army about AFSPA etc, I have to admire and salute the amazing job being done by them (Army), Air Force, ITBP," Omar wrote on micro-blogging site Twitter.
He said everyone must appreciate the massive rescue operations launched by these agencies in Uttarakhand.
"The kind of operation they have mounted to rescue people in #Uttarakhand, with no glory grabbing is something we must all salute," he tweeted.
"I did NOT fear a L&O (Law and order) disturbance from the writings on the mountain nor did I call them 'disgusting'. Change your sources," he said.
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The reports in a section of media claimed that Omar had expressed displeasure over the graffiti on the hills and directed the Divisional Commissioner, Kashmir, to take action required under law.
The reports also claimed that the official concerned had issued notices to the Army in this regard.