The National Human Rights Commission said the turmoil in Kashmir was "augmented by trans-border terrorism and jihadi funding from the neighbouring country", in a veiled reference to Pakistan.
"The turmoil in Kashmir is on the spotlight now... The use of plastic pellets by CAPFs (Central Armed Police Forces) is controversial.
"The NHRC has taken up a case on the matter but withholds its comments now because human rights of both sides are involved, when young crowd pelt stones at police personnel," the rights panel says.
The NHRC report has been submitted to the UPR Working Group.
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The use of pellet guns by security personnel to control the crowd has been at the centre of a raging debate.
The Commission also said there was a 17 per cent rise in communal violence in 2015 as against 644 in 2014. The Communal Violence (Access to Justice and Reparations) Bill 2013, was yet to become law, it added.
"Sporadic instances of violence concerning eating of beef have been reported. The fringe wing of Hindutva brigade is alleged to be behind these incidents which are few and far between.
"Though disquieting, it is too early to assess whether they could be a threat to secular and pluralistic structure of Indian society," NHRC said.
The rights body also slammed the government for not ratifying the UN Convention Against Torture (CAT).
The Commission says, "The legal system continues to be dysfunctional with slow disposal of cases and inordinate delay in giving finality to both criminal and civil litigation."