During a meeting held in Hyderabad on May 31, 2025, Telangana Health Minister C. Damodar Raja Narasimha raised concerns over delayed stipend payments and strained infrastructure in private medical colleges. In response, NMC Chairman Dr. B.N. Gangadhar assured that the Commission would look into these issues, including potential temporary exemptions in building norms and expansion of postgraduate seats to address faculty shortages.

An investigation by The Probe revealed that the National Medical Commission continued rejecting appeals from victims of medical negligence by citing outdated and withdrawn regulations, despite the reinstatement of more protective rules for patients. This practice not only misled the Supreme Court but effectively deprived patients of their legal right to challenge adverse decisions.

In the 2023 regulatory update, the National Medical Commission removed key appeal rights for patients in cases of medical negligence by eliminating provisions for legal representation and appeal for victims, while preserving appeal routes for medical practitioners. This disparity has led to a Public Interest Litigation challenging the imbalance in access to justice.

The National Medical Commission notified professional conduct regulations concerning the mandatory prescription of generic medicines on August 2, 2023, with penalties including up to a one-month suspension of a doctor's license for non-compliance. The measure has been widely criticized for its heavy-handed, top-down approach which critics argue could undermine physician autonomy and compromise drug quality, raising alarms about authoritarian regulatory practices.

Multiple instances, including failure to publish asset declarations and ignoring RTI applications and appeals, highlight significant transparency and accountability issues at the National Medical Commission.

The National Medical Commission Bill was passed by the Lok Sabha on 29 July and the Rajya Sabha on 1 August 2019, prompting significant criticism and protest from doctors, medical students, and professional associations over concerns of centralized regulatory overreach and potential threats to professional autonomy.