The Council is a supreme decision making body of the Institute. Being at the helm of affairs, it is responsible for overall management of the Institute. The Council performs its responsibilities under the Act and Regulations which authorizes it for managing resources /affairs of all kinds. The Council is for three years. It is comprised of twelve members out of whom eight members are elected by the members of the Institute and four members are nominated by the Government of Pakistan. The nominees usually belonged to Ministry of Finance (MoF), Securities and Exchange Commission of Pakistan (SECP), Auditor General of Pakistan (AGP), Federal Board of Revenue (FBR), State Bank of Pakistan (SBP) and any other government regulatory bodies.

The office bearers of National Council comprised of President, Vice President, Secretary and Treasurer, who are elected from amongst members of the Council. The President acts as Chief Executive of the Council.