While Mallya is facing financial troubles of his own, Roy has been behind bars with Sahara Group unable to raise cash to get its chief out on bail.
Mallya, speaking ahead of the Mexican Grand Prix this weekend, said the "unfortunate" situation is not affecting the team.
"I am very happy with Sahara Group as partners. There is no issue at all. I feel very sorry for Subrata Roy but this unfortunate situation is not affecting the team in anyway. Our partnership stands strong," Team Principal Mallya told PTI.
It will be fair to say that the team has continued to punch above its weight despite the issues its owners face off the track. Force India have managed to be consistently among points ever since introducing their B-spec car in Silverstone with Sergio Perez delivering the team's third ever podium at Sochi being the highlight so far.
"It is something we are very proud of (the team's performance graph since 2008). We have got three podiums now with the last one coming at Sochi. We are hoping for a similar result in Mexico to further strengthen our fifth place in the team standings," said Mallya of his squad which is on its way to finish fifth for the first time.
Aware of the repercussions, Mallya said it is tough to predict the outcome of the case.
"I mean nobody can predict the outcome of a European Union complaint. We have filed a complaint because we believed the distribution of income in Formula 1 is not fair, it is disproportionate. Now it is up to the commission to take whatever action they want to take.
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