Police in the capital New Delhi, where a farmers' tractor rally last Tuesday turned into a deadly rampage where one person died and hundreds of police officers were injured, said they had filed a complaint against the toolkit's makers.
The complaint does not name Thunberg.
"Preliminary enquiry has revealed that the 'toolkit' in question appears to have been created by a pro-Khalistani Organisation 'Poetic Justice Foundation'," police said in a statement, citing Sikh separatists who want to create a homeland of Khalistan in India's northern Punjab state.
Many of the protesting farmers hail from Punjab.
Police said the toolkit creators appeared to "create disharmony among various social, religious and cultural groups and encourage disaffection and ill-will against the (government) of India".
The toolkit shared by Thunberg offers basic advice including joining on-the-ground protests and showing support on social media.
Thunberg tweeted late Thursday that she still supported the protests. "No amount of hate, threats or violations of human rights will ever change that," she added.
Earlier Thursday, a delegation of opposition lawmakers were blocked from meeting farming unions at one of the protest sites by police.
"Even MPs are not being allowed to meet peacefully protesting farmers. This is truly a black day for democracy!" Harsimrat Kaur Badal, a lawmaker and former government minister from Punjab, tweeted.
Modi has said the laws are necessary to modernise India's agriculture sector, but farmers fear they would be placed at the mercy of big corporations.
The protests have become one of the biggest challenges to Hindu nationalist Prime Minister Narendra Modi since he took power in 2014.