The government’s late-night intervention into the war taking place within the Central Bureau of Investigation has only made matters even more confusing. A day after a newspaper headline said “CBI goes after CBI,” describing how the Central Bureau of Investigation had raided its own office in Delhi the previous day, the Centre stepped in to put the two warring officers – director, Alok Verma, and special director, Rakesh Asthana – on leave. It appointed M Nageshwar Rao the interim director, through the Appointments Committee of the Cabinet, in orders that were reportedly issued at around 11:30 pm.

A short recap: CBI director Alok Verma has accused special director Rakesh Asthana of accepting bribes. The Delhi High Court on Tuesday said no coercive action can be taken against Asthana till October 29, when it will resume hearing the officer’s plea to quash the CBI’s First Information Report against him. Before that, Asthana on this part had had accused Verma of political favouritism and impeding the functioning of officers who are investigating corruption.

Such allegations of corruption at the top are not new for the CBI. Over the last few years, two of its directors, Ranjit Sinha and and AP Singh, have been implicated in corruption cases. But the current fracas goes beyond individual corruption and political manoeuvring. It reveals a serious institutional crisis. Making it worse is the fact that the government has left it festering for such a long time.

Like everything involving the CBI, matters are highly politicised. Asthana is seen as being close to Prime Minister Narendra Modi and was hand-picked for the post, despite allegations of corruption against him by the non-governmental organisation Common Cause. Asthana had earlier served in the Gujarat police and investigated the burning of the Sabarmati Express at Godhra in 2002, the act that started the Gujarat riots and came to define Modi’s tenure as chief minister.

The fact that the CBI is politicised, acting less like an investigative agency and more like an organ of the party in power is well known. During Prime Minister Manmohan Singh’s tenure, Modi himself described the CBI as the “Congress Bureau of Investigation”. In 2013, the Supreme Court called it a “caged parrot”, given the alleged use of the agency by the Congress to cover up irregularities in the allocation of coalfield licences to private companies.

That the agency behaves in an arbitrary manner is not surprising either, given its origins. The agency was set up not by a law but by a simple a Union Home Ministry resolution in 1963. Moreover, the existence of the CBI ignores the Indian Constitution, which places the power of policing firmly with the states. For these reasons, the Gauhati High Court in 2013 held the agency to be unconstitutional. However, that order was stayed by the Supreme Court, which is still to decide on the merits of the case.

Until Tuesday, it seemed unclear what the government would do about the situation, with Modi summoning both the warring officers to talk over the issue. Then, on Tuesday night, it only added more confusion to the matter. As per the Lokpal Bill, the CBI Director is supposed to be independently appointed by a committee including the prime minister, the Chief Justice of India and the Leader of the Opposition, and once that is done, the director has a fixed two-year tenure. If the government can simply send him on leave, and get the Appointments Committee of Cabinet, to have someone else play interim director, what use is the fixed-tenure rule in the first place?