The CCI, which is yet to complete its investigation, fined Monsanto for delays in filing replies, according to official documents reviewed by Reuters.
Monsanto responded to CCI's queries in August, but only after eight reminders issued between April 2016 and May this year, the watchdog's November order showed.
"The commission hopes and trusts that full cooperation shall now be provided," the CCI said in its order dated Nov. 14.
A Monsanto India spokesman said: "Monsanto continues to extensively cooperate with the CCI in the investigation and has been providing information in response to requests received."
"This order is related to a procedural matter and is subject to further orders from the Delhi High Court," he added.
Challenging the role of CCI and the nature of its probe, Monsanto has filed two separate cases with the Delhi High Court.
Monsanto is locked in a battle with Indian seed maker, Nuziveedu Seeds Ltd, one of the complainants at the CCI.
That battle sparked a series of government moves that prompted the world's biggest seed company to withdraw from some businesses in India, one of the world's most important seed markets, Reuters reported earlier this year.