CBI sources said the agency has registered a case against Khan and unknown officials for alleged criminal conspiracy and corruption.
The action has been taken on the basis of a complaint received from tax authorities, they said.
The sources refused to give any further details stating it may affect their probe.
The Enforcement Directorate (ED) also registered a fresh case of money laundering against Khan, six years after he was booked on the same charges under the Prevention of Money Laundering Act (PMLA).
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The fresh FIR by the Enforcement Directorate (ED) against Khan, touted to be one of the highest tax evaders of the country, is significant as sources said some "fresh evidence has been found" by investigators which includes sensitive information received from foreign shores.
The new complaint against Khan comes after about six years as he was first booked by the ED in 2011 under PMLA and was then arrested too.
The role of certain I-T department officials who probed this case is also under the scanner of the agency, they said.
It is expected that the two agencies could launch fresh action of searches and questioning in this case, which has beentalked about as one of the most important black money cases ofthe country.
The Khan case is the only one listed by name in the terms of reference of the Special Investigation Team (SIT) on black money that was constituted by the government in 2014 on the directions of the Supreme Court.
He was also questioned by a top level team of the ED and CBIofficials last year after this action.
The stud farm owner, based in Pune and Mumbai, came under
the scrutiny from multiple agencies including the Economic Offences Wing of the Mumbai Police in 2007 which had been probing him and his associates on charges of money laundering, income tax evasion and violations of thePassport Act.
However, an order by the Income Tax Appellate Tribunal (ITAT) last year had pegged his tax liability at about Rs 75 crore.
The ED had also attached few immovable assets of Khan under PMLA as part of its probe against him, his wife Rheema and others.