The institution's leadership went after Dr. Animesh Roy in 2009 for blowing the whistle on scientific misconduct. You have to read The Telegraph report by G. Mudur -- Science's Ugly Underbelly to get a sense of how ugly it really was.
Nearly three years later, its leadership has dismissed Dr. Nilanjan Roy allegedly for blowing the whistle on misconduct in financial matters. Rahul has a post (with links) summarizing this case.
The first case came to an end after Dr. Animesh Roy was reinstated in 2011. It is horrible to even imagine the kind of ordeal he went through during those 2+ years -- just because some higher-ups at NIPER felt that their egos were hurt by his allegations.
From news reports, the second case is also likely to go in favor of the whistleblower. It'll leave a deep, shameful scar on the institution if this eventuality arrives after inflicting personal and professional damage to Dr. Nilanjan Roy.
Those at the helm at NIPER, especially its Board members and their chairman, Dr. V.M. Katoch, have to do the right thing. NIPER's institutional reputation is at stake.