These websites were carrying pro-Khalistani and anti-India content.
"12 websites have been ordered to be blocked by the Ministry of Electronics and IT under section 69 A of the IT Act. They were supporting pro-Khalistani activities. The order was issued on Monday," the source - who did not wish to be identified - told PTI.
The Ministry of Electronics and Information Technology (MEITY) is the nodal authority for monitoring the cyberspace in India.
According to the PTI report, the banned websites include SFJ4Farmers, pbteam, seva413, pb4u, sadapind, among others with "org" extension.
"Your requested URL has been blocked as per the directions received from Department of Telecommunications, Government of India. Please contact administrator for more information," some of the banned websites said.
The Home Ministry had last year banned SFJ for its anti-national activities.
SFJ had aggressively pitching for Sikh Referendum 2020 as part of its separatist agenda.
The move comes after government had blocked 40 websites in July belonging to SFJ for supporting secessionist activities inside and outside India.
SFJ’s lead campaigner of the secessionist movement, Gurpatwant Singh Pannu, has been declared a terrorist by the Union Government under the Unlawful Activities (Prevention) Act.