New Delhi's comments came after UN High Commissioner for Human Rights Zeid Ra'ad Al Hussein reportedly said at the the start of the 33rd session of the Human Rights Council that a team from the Geneva-based Office of the High Commission for Human Rights (OHCHR) should visit Jammu and Kashmir in the wake of large-scale violence.
Over 80 people have died in the violence following the killing of Hizbul Mujahideen terrorist Burhan Wani in July.
"We have seen the comments by the UN High Commissioner for Human Rights on the situation in the Indian state of Jammu and Kashmir," the External Affairs Ministry said in a statement..
"We note that he has received conflicting narratives on the cause for the confrontations," it stated.
The ministry said that the present situation in Jammu and Kashmir "arose from the death of a self-acknowledged commander of the terrorist organisation, Hizbul Mujahideen, who was wanted for several terrorist acts".
"It was further aggravated by sustained cross-border terrorism emanating from Pakistan," the statement said.
Stating that terrorism was the grossest violation of human rights and should be so acknowledged by any impartial and objective observer, it said: "The high number of casualties sustained by Indian security forces is a reflection of the tremendous restraint they have displayed in difficult circumstances."
Regarding the suggestion for a visit of an OHCHR team to both sides of the Line of Control, New Delhi made it clear that "we would underline that there is no comparison between the situation in the Indian state of Jammu and Kashmir and Pakistan-occupied Kashmir".
It said while Jammu and Kashmir has a democratically elected government, Pakistan-occupied Kashmir "has seen a Pakistani diplomat arbitrarily appointed as its head".
Earlier on Tuesday, Pakistan welcomed Al Hussein's suggestions for a OHCHR team's visit to Jammu and Kashmir.
"We strongly support the High Commissioner's position that an OHCHR team should visit Indian-occupied Jammu and Kashmir to independently investigate the grave human rights violations being perpetrated by Indian occupation forces, resulting in the killing of more than 90 civilians and 8000 injured, including those with severe pellet gun injuries," the Pakistan Foreign Ministry said in a statement.
"The visit by the OHCHR team would help to end the culture of impunity which is prevailing for more than 68 years in IOK, in violation of international law and UN Security Council resolutions."
New Delhi, in its statement, made it clear that "the Indian state of Jammu and Kashmir is part of a pluralistic and secular democracy, where freedoms are guaranteed by an independent judiciary, an active media and a vibrant civil society".
"In contrast, Pakistan-occupied Kashmir is administered by a 'deep state' and has become a hub for the global export of terror," it stated.
Stating that the issue of an external mission was considered by an all-party conference on August 12 that met to discuss the situation in Jammu and Kashmir, it said: "It was unanimously felt that Indian democracy has all that is required to address legitimate grievances."
On the basis of that, it said, an all-party delegation visited Srinagar.
"Despite cross-border terrorist infiltration that saw an encounter only yesterday, government remains fully engaged in normalising the situation as soon as possible," the External Affairs Ministry stated.
"We hope that the connection between terrorism and violation of human rights would be recognised and deliberated upon in Geneva," it added.
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