Amit Shah was among those who championed an anti-conversion law that harasses Christians, the report says.
BJP president Amit Shah has been named in the latest report of a US government body monitoring international religious freedom.
The report of the US Commission on International Religious Freedom says that Mr Shah was among those who championed an anti-conversion law that harasses Christians.
"Naming the BJP president, I would reject that completely because that comes from a very flawed and even a lack of understanding of the Indian constitution... They should read on it before they make a comment on it," said the BJP's Nalin Kohli.
The agency's members were denied a visa to travel to India in March, with the government saying the group has no business judging the situation in the country.
The new reports say that last year, religious tolerance in India deteriorated and that groups that intimidated and attacked minorities were "tacitly supported" by members of the BJP who used "religiously-divisive language to further inflame tensions". The document singles out BJP parliamentarians Yogi Adityanath and Sakshi Maharaj for fuelling hate campaigns against Muslims.
It also says that in May last year, a meeting of Christians that had been cleared by Madhya Pradesh officials found its permission revoked "due to what the community believes was RSS pressure".
India has said that it does not need a US agency to either judge or endorse the religious and other freedoms it pledges to citizens.