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ORF

Indian Society of International Law

Centre for Policy Research

Carnegie India

Centre for Internet and Society

Asian African Legal Consultative Organisation

PRS Legislative Research

Migration and Asylum Project

Centre for Communications Governance

Human Rights Law Network

Naz Foundation

And many more which I can't recall at this moment
Adding to this,

Centre for Civil Society

CLPR

Some centres of JGLS that are headed by good faculties
Not Vidhi, please. It’s actually better to intern with a prof at NLSIU or Jindal with a foreign degree who can write you a letter of recommendation if you apply for a master’s degree. These universities also have greater name recall among foreign universities than Vidhi.
Barely any NLS or JGLS prof is recognised even in India, let alone abroad. Vidhi gets a lot of govt policy advisory mandates. The latter is always better when it comes to foreign recommendation.
What about NLUD? Can you suggest some good centres to intern with other than P39A?