The affidavit, submitted by CBI director Ranjit Sinha, says that the Prime Minister's Office and Coal Joint Secretary removed part of paragraph on non-existence of specific weightage or points in the system of allocation.
The Law Minister deleted finding on non-preparation of broadsheets or charts by the screening committee. The Law Minister also deleted a sentence on finding on scope of inquiry on legality of allocation.
But the CBI has emphasised that a draft status report was shared with the political executive and the Attorney General, not the status report it submitted to the court in sealed cover a few days later.
The affidavit claims that no names of suspect or accused were removed from the status report and also that no suspect or accused were let off in the process.
It also says that consequent changes in the report have neither altered its central theme nor shifted the focus of inquiries in any manner.
It is, however, difficult at this stage to attribute each change to a particular person with certainty, according to the affidavit.
The CBI affidavit also names officials of PMO and Coal ministry, who had perused the draft report and on whose suggestions changes were made in it. Mr Sinha said Shatrughan Singh and A K Bhalla, the joint secretaries in PMO and ministry of coal respectively were "in regular interaction" with his officers with regard to ongoing inquiry in the coal scam.
The CBI chief also extended an unconditional apology to the court for any inadvertent omission or commission and assured it of an independent probe in the coal scam.
The Supreme Court had, after a stinging critique of the CBI last week, asked the agency for crucial details of a meeting at Mr Kumar's office a few days before the report was submitted, where the minister allegedly vetted it.
Sources say Law Minister Ashwani Kumar met Prime Minister Manmohan Singh to explain the latest developments. Mr Kumar told the PM that the government, which is reeling under the massive coal scandal, will emerge stronger after the Supreme Court's next hearing on Wednesday, the sources added. (Read: After CBI submits affidavit, Law Minister meets PM)