Alok Verma has challenged his removal in the Supreme Court which will hear his case on Friday

Highlights Alok Verma was replaced as the top boss of the CBI

M Nageswar Rao took charge as the new CBI chief

Government said it was done to maintain CBI's integrity

Alok Verma, the CBI chief who has been exiled into leave, has told the Supreme Court that the autonomy of the country's premier investigating agency is being compromised and by malintent that includes when "certain investigations into high functionaries do not take the direction that may be desirable to the government".

Mr Verma was replaced as the top boss of the CBI in a 1 am coup that saw the CBI headquarters in the capital being cordoned off by the police before the man chosen as the new CBI head, M Nageswar Rao, drove in and took charge.

Like Mr Verma, the CBI's No. 2 officer, Rakesh Asthana, has also been sent on leave; this was necessitated to "maintain the CBI's integrity", claimed Finance Minister Arun Jaitley on Wednesday. The minister cited the public feud between Mr Asthana and Mr Verma - both men have accused each other of accepting bribes worth crores by men being investigated by the CBI. Earlier this week, the CBI named Mr Asthana as an accused in an FIR; yesterday, he asked the Delhi High Court to cancel that FIR or police case; it did not do that, but it banned the CBI from arresting him till Monday, when it will next hear the case.

Mr Verma has challenged his removal in the Supreme Court which will hear his case on Friday. His petition says that Mr Asthana "concocted evidence" against him to accuse him of corruption and that he was inevitably at odds with the opinion of majority officers in sensitive cases.

"Not all influence that is exerted by the political government would be found explicitly or in writing. More often than not it is tacit and requires considerable courage to withstand," says the petition. Mr Verma also promises to give details of "many cases that have led to the present circumstances".

The opposition has alleged that Mr Verma has been sent on leave - effectively sacked - because he was weighing an inquiry into India's purchase in 2015 of 36 Rafale fighter jets from France; earlier this month, Mr Verma personally met with Arun Shourie, Prashant Bhushan and Yashwant Sinha, all critics of the Modi government, when they filed a complaint about corruption in the Rafale deal; his in-person greeting of them to accept their complaint had angered the government, NDTV had reported.

Mr Asthana is known for his proximity to BJP chief Amit Shah and Mr Verma's removal today is seen as a major victory for him. Mr Asthana was made No. 2 in the CBI though he was tainted by allegations of accepting favours and bribes and was named in six cases being investigated by the CBI. While a senior police officer in Gujarat, he handled the case involving the Godhra train burning, which led to three-day communal violence across Gujarat in 2002, and the Sohrabuddin Sheikh fake encounter case, in which Amit Shah was discharged.