Ferrari this week sparked a furore by opting to display the emblem on the chassis of the F2012s driven by Fernando Alonso and Felipe Massa.
In a statement on their website the Maranello marque claimed the move was "in the hope the Indian and Italian authorities will soon find a solution to the situation currently involving two sailors from the Italian Navy".
Two members of the Italian navy's vessel protection department are currently awaiting trial following the death of two Indian fishermen in February.
As part of a detachment serving on board oil tanker Enrica Lexie, it is alleged by Indian authorities that the two sailors shot and killed the fishermen in waters off the coast of southern India, believing them to be pirates.
Ferrari's decision to sport the flag on their cars, despite the very carefully-worded nature of their statement, has been interpreted by the likes of the Indian ministry of external affairs as political.
The current statutes of motor sport's governing body, the FIA, make it clear there should be no political discrimination.
But following a meeting on Saturday between Ferrari team principal Stefano Domenicali and FMSCI president Vicky Chandhok, the latter is happy to accept the former's stance.
Chandhok said: "The FMSCI would like to maintain that the FIA code of motorsport is apolitical and non-religious and the FMSCI will not permit motorsports to be politicised in any manner.
"Stefano Domenicali has confirmed their initiative of carrying their national navy flag does not have, and should not be seen as, having any political implication.
"FMSCI firmly believes carrying their national navy flag will not have any effect on the case pending before the Indian courts.
"The FMSCI will not permit any attempt to subvert the process of justice by politicising the event."