The chief of India's federal investigation agency and his deputy were removed after months of infighting that saw the pair accusing each other of corruption. (Photo: PRAKASH SINGH/AFP/Getty Images)

Prime minister Narendra Modi’s government on Wednesday (24) removed the chief of India’s federal investigation agency and his deputy after months of infighting that saw the pair accusing each other of corruption.

Alok Verma, the director of the Central Bureau of Investigation (CBI), and his second-in-command Rakesh Asthana were relieved of duty pending inquiry, the government said in a statement.

Both men had levelled “grave allegations of corruption” against one another, risking a “potential loss of credibility and reputation” to the agency.

The government took the unusual step of intervening because of “extraordinary and unprecedented circumstances” at the CBI, including Verma refusing to hand over documents as part of a government inquiry into misconduct.

Verma last week launched a bribery investigation into Asthana, accusing him of taking bribes to stymie a probe into an exporter facing charges of money laundering and tax evasion.

Asthana had already accused his boss of taking kickbacks in the same case.

The government, in standing down both men, also quashed Verma’s inquiry into alleged corruption involving his deputy and ordered investigators to stand down.

The head of that unit was transferred to a post in the Andaman Islands – a remote Indian territory in its seas to the east.

Verma has appealed his dismissal at the supreme court, which will hear his appeal on Friday (26).

The court has in the past described the CBI – the Indian equivalent of the FBI – as a “caged parrot”, one constrained in its inquiries by the ruling party of the day.

The agency has the authority to pursue high-profile individuals or cases deemed outside the reach of local police.

India’s opposition, including the Congress Party, accused Modi’s Bharatiya Janata Party (BJP) of overreach and trying to control the agency.

India’s Finance Minister Arun Jaitley rebuffed suggestions the government had acted in self-interest.

“The CBI is our premier investigative agency. And the maintenance of its institutional integrity is absolutely essential,” he told reporters in New Delhi.

The government appointed Asthana to the CBI deputy post last year.

Before that, he spent decades as a high-ranking police official in Gujarat, including during Modi’s more than decade-long tenure as chief minister of the state.