Asked whether the FIR has been registered against Thunberg, Special CP (Crime) Praveer Ranjan said nobody has been named in the case.
The case against unnamed persons have been registered on charges of criminal conspiracy, sedition and various other sections of the Indian Penal Code, he said.
The senior Delhi Police officer said initial investigation has suggested the document's link with a pro-Khalistan group, named ''Poetic Justice Foundation''.
He said considering the unfolding of events in the past few days, including the violence on January 26, it has revealed "copycat execution" of the action plan mentioned in the ''toolkit'' which was also aimed at waging "a social, cultural and economic war against the Government of India."
The Delhi Police's comments come in the backdrop of support extended by global celebrities such as singer Rihanna and Thunberg to the farmers'' protests against the three farm laws.
Lending her support to the farmers'' agitation, the teen activist had shared "a toolkit for those who want to help".
"Here's a toolkit if you want to help," tweeted Thunberg, which takes the user to a document containing details on ways to support the protest.
On Thursday, the teen activist took to Twitter, saying, "I still #StandWithFarmers and support their peaceful protest. No amount of hate, threats or violations of human rights will ever change that. #FarmersProtest."
Ranjan said in the process of monitoring the social media, they have also come across "one particular document which was uploaded by one social media handle on a particular platform."
"This toolkit has a particular section which says --- digital strike through hashtags on or before January 26, tweet storms on January 23 onwards, physical action on January 26 and watch-out or join farmers march into Delhi and back to borders," Ranjan told reporters.
He said if someone goes by how the events unfolded, including the violence on January 26, it reveals a "copycat execution of the action plan mentioned in the "toolkit".
"The Delhi Police has registered a case under section 124-A, 153-A, 153 and 120-8 IPC. The Cyber Cell will investigate the case," he said, adding that the farmer leaders were made aware of these organisations having vested interest during the process of negotiations by Delhi Police.
"The document ''toolkit'' was aimed to spread disaffection and ill-will against the Government of India and creating disharmony among various social, religious and cultural groups," Ranjan told reporters.
"The Delhi Police has been monitoring social media where it has identified over 300 social media handles which have been used for pushing hateful and malicious contents," the senior officer said.
In the context of the Kisan agitation, while the farmers may not even be aware as to what forces are guiding their actions and setting their agenda, there were clear indicators that hostile deep "state actors" were either behind it or would join in to exploit the sentiments, Ranjan said in a statement.
Rihanna, among the biggest pop stars of the day with 101 million followers on Twitter, started the global chorus of support for India's farmers, taking their movement to a new high.
"Why aren't we talking about this?! #FarmersProtest," she tweeted, linking a CNN news article on the internet shutdown around New Delhi as protesters clashed with the police.
India on Wednesday hit out at global celebrities such as singer Rihanna and Thunberg for their support of the farmers’ protests, the focus of a sharply polarised international debate that saw several Bollywood and cricket stars and top ministers rally around the government in its pushback.