The deputy also called on Britain and the EU to address the issue, saying they "must both increase pressure on the Indian government to end human rights abuses in Kashmir."
Her demand coincides with publication of a report by Brussels-based Human Rights Without Frontiers (HRWF), a leading rights NGO, which outlines areas where it says religious minorities are under threat.
It says the "most dangerous" countries for religious minorities are Iran, China and North Korea, while among the groups "most targeted" are Falun Gong practitioners in China.
In highlighting the case of Kashmir, McIntyre has listed recent instances of violent oppression including rape, arrest, murder and indiscriminate use of birdshot against protesters.
The Tory deputy said she wanted to send a "strong message of condemnation" over what is happening in Kashmir, and called on the government of India to "end this occupation, stop the persecution and, crucially, to remove the immunity of its military from prosecution for their crimes."
McIntyre, who co-chairs the European Parliament's Friends of Jammu Kashmir group, was a keynote speaker at recent seminar in the UK on the issue.
She has also warned that Britain's decision to leave the EU would create fresh challenges for the human rights campaign.
The ECR group member explained: "Most members of the friends group are British; but we will be leaving within a few years because of the referendum."
She added, "The group therefore must be turned into a truly international cross-party group before then, so that its work will continue effectively post-Brexit.
"In addition, outside the EU, the UK will be entirely responsible for our own foreign policy, so we must encourage our own government to be strong.
"We must say to India - of course we want to trade with you, but not at any price. We must tell them they are not abiding by the Geneva convention. We must make it clear we will not stand by and see them continuing to maim, to blind and to kill."
Meanwhile, in a separate report, HRWF has highlighted alleged rights abuses in Thailand, which recently approved a new constitution in a referendum.
The NGO cited the case of 25-year-old Jatupat Boonyapatraksa, who is continuing his hunger strike at a Thai prison in protest against the country's "broken justice system."
Jatupat was arrested on 6 August for distributing anti-constitution flyers. HRWF has joined campaigners in asking Thai people to write postcards calling for the government to drop charges against him.
Several MEPs, including Charles Tannock and David Martin, have been critical in the past of the human rights situation in Thailand.