Mr Sharma and his son Ramesh Sharma were killed on February 25, 2017, while Mr Gupta was murdered on April 23, 2016.
The charge sheets were filed in the special court in Mohali on May 19 under various charges dealing with criminal conspiracy, murder, and common intention under the Indian Penal Code and under various provisions of the Unlawful Activities (Prevention) Act and the Arms Act.
The agency has named Hardeep Singh alias Shera, Ramandeep Singh alias Bagga, Dharminder Singh, Anil Kumar, Jagtar Singh Johal, Amaninder Singh, Manpreet Singh, Ravipal Singh, Pahad Singh, Parvez alias Farru, Malook Tomar, Harmeet Singh, Gurjinder Singh, Gursharanbir Singh and Gurjant Singh Dhillon as accused in the case.
"All the persons targeted belonged to certain specific communities and organisation. The objective of the conspiracy was to destabilize the law and order situation in Punjab and to revive the fledgling terrorism in the state," it added.
The probe agency said that during the investigation, it was found that the conspiracy had its foot-prints in several countries including Pakistan, Britain, Australia, France, Italy and the UAE. As part of the conspiracy, large amounts of funds were supplied to the perpetrators through Italy, Australia and Britain.