Six others, including the then PWD minister Churchill Alemao, were also listed in the charge sheet in the scam in which the US firm has been charged with bribing Indian officials to win two water developmental projects in Goa and Guwahati.
The charge sheet, running into around 1,000 pages, was filed by Crime Branch before special court in Panaji.
Police also named Louis Berger official James McClung, former India Vice-President of the company Satyakam Mohanty, head of (Japan International Cooperation Agency) JICA-aided project in Goa Anand Wachasunder, suspected Hawala dealer Raychand Soni and former Margao municipal council chairperson Arthur D'Silva.
The accused are charged under section 201 (causing disappearance of evidence of offence or giving false information to screen offender), 120-B (criminal conspiracy) of IPC, and under sections 7,8 and 13 of the Prevention of Corruption Act.
On July 21, 2015, the Crime Branch had registered an FIR against unknown ministers of then Congress government of 2010.
The alleged bribery had come to light after Louis Berger company admitted to the violations under US Foreign Corrupt Practices Act and agreed to pay penalty of USD 17.1 million to resolve the charge that it had bribed foreign officials.
The Rs 1,031-crore project, funded by JICA, was approved when the Digamber Kamat government was in power for augmenting water supply in south Goa and laying sewerage lines in the state's major cities.
Louis Berger was part of a consultancy consortium appointed by two Japanese firms and an Indian partner for managing the $311 million Goa Water Supply and Sewerage Project awarded in 2009.
Crime branch had interrogated Kamat many times during the probe. He had secured anticipatory bail from local court on August 19, 2015.
Alemao was arrested on August 5, 2015 after he was called by crime branch officials to record his statement.
In the interim charge sheet filed on September 29 last year, police charged Alemao and others under various sections of IPC and Prevention of Corruption Act.
Kamat's name was not included in that charge sheet though he was shown as a suspect. In the charge sheet filed on Thursday, the crime branch has termed Kamat as the prime conspirator.
"Kamat was instrumental in aiding then PWD minister Churchill Alemao in formation of different committees by approving the same for JICA project, contrary to JICA guidelines.
"Prime conspirator Digambar Kamat is also the criminal conspirator in concealing the main noting file of awarding JICA consultancy in Goa in connivance with other co-accused Alemao in order to hide the notings in the main file which would put light on the misdeeds of accused Wachasunder," the charge sheet stated.
The charge sheet further said that documents of "immense wealth in crores and different bank accounts accumulated by Kamat all over India in his name as well as his proxy has been traced and scrutiny of the same will be done upon custodial interrogation of Kamat."
His anticipatory bail has been challenged by police in the Supreme Court.
"Upon scrutiny of all the documents of the properties and bank accounts in different banks all over India, corroborative evidence will be submitted before the court as per provisions of CrPC," the charge sheet stated.