Taking exception to Shinde's statement, Dal Khalsa president HS Dhami said it was just "customary rhetoric" aimed at portraying Sikhs in bad light.
He said the home minister's views were "baseless, unfounded and ridiculous" and meant to mislead the public.
Shinde had made the statement during his address at the chief ministers' conference on internal security held in New Delhi on Wednesday.
The Dal Khalsa also criticized Punjab Deputy Chief Minister and Shiromani Akali Dal president Sukhbir Singh Badal for remaining a "mute spectator" when Shinde made the remarks.
"Why Sukhbir did not register his dissent and objection there and then," Dhami asked.