Justice RM Lodha called the agency a "caged parrot" and "its master's voice" after it was revealed that the CBI presented a draft report of its investigation into the scandal to government officials before submitting it to the Supreme Court last year.

On Monday, CBI director Ranjit Sinha provided the Supreme Court with a nine-page affidavit detailing who the draft was presented to and what changes were made.

The Indian Express reported that CBI Director Ranjit Sinha cited in his affidavit two "significant" changes made in the report after the Law Minister's intervention but neither of the changes made have "altered the central theme of the report, nor shifted the focus of inquiries or investigations in any manner”

The affidavit stated that "no names of suspects or accused were removed... no accused or suspects were let off in the process" and there was "no deletion of any evidence" against anyone.

But Judge Lodha disagrees, stating in court that the "heart of the report" had been altered, a damning statement for the CBI which proudly proclaims its motto to be "Industry, Impartiality and Integrity".

The Supreme Court judge's statement gave, for the first time, an authoritative voice to opposition complaints that for years India's Congress party-led government had been using the investigating agency to mask wrongdoing.

However, two former CBI directors told Reuters that the agency was subject to political influence, irrespective of which party happened to be in power at the time.

When the hearing began earlier in the week, the top court said it would seek to free the federal investigation body from political interference, according to Bloomberg.

The court hearing has severely disrupted parliament and prime Minister Manmohan Singh is now being called on to step down.

The scandal was exposed when, in March 2012, a leaked government audit suggested the state had squandered more than $US200 billion by allocating coal blocks instead of allowing competitive bidding.

The report, which the Times of India called “mind-boggling”, ruffled reformers within the Indian coal industry, led to the opening of public coal block auctioning and recently resulted in direct corruption accusations against the country’s chief of government.

The CBI report was an investigation into the matter.