Mitesh Amin, counsel for Amit Shah, in Gandhinagar on Friday. (PTI)

Ahmedabad, July 23: The CBI today filed charges of murder and criminal conspiracy against Amit Shah in the Sohrabuddin fake encounter case even as a special court turned down his anticipatory bail plea.

The Gujarat junior home minister and Narendra Modi confidant can now be arrested at any minute unless he gets bail from the high court.

Shah did not appear before the CBI for the second consecutive day, possibly fearing that he would be arrested at the end of questioning. The CBI had issued him two summons, both of which he ignored.

Instead of Shah appearing before the CBI by 1pm today, his counsel, Mitesh Amin, showed up around 12.45pm. Amin requested the CBI to hand him a questionnaire and sought more time to prepare the response to the five-year-old case.

The CBI, however, turned down Amin’s request, saying a person who had been issued summons could not be given a questionnaire because that was not the way the agency functioned. Amin then applied for Shah’s bail, but that too was rejected.

Sources said Shah, who has been missing over the last few days, may have ignored the summons a second time to delay his possible arrest. In a statement yesterday, he had said he would appear before the CBI and co-operate with it.

Around 2.30pm, CBI officials visited Shah’s office to track him down. But his personal secretary told them he was “clueless” about his boss’s whereabouts. In the last few days, Shah has skipped four cabinet meetings, has not used his official car and has kept his mobile switched off.

In the 77-page chargesheet, the CBI named Shah as an accused, along with two of his aides who have not been arrested yet. The aides are Ajay Patel and Yashpal Chudasama, respectively the director and chairman of the Ahmedabad Co-operative District Bank. Shah has been charged with murder, criminal conspiracy to abduct and destruction of evidence.

The timing of the chargesheet is linked to Abhay Chudasama, one of three senior Gujarat police officers held in the case. Since the chargesheet had to be filed within 90 days of Chudasama’s April 28 arrest, it was done today, CBI officers said.

A rights group, Jansangharsh Manch, today urged the Gujarat governor to remove Shah as minister. But he appears to have the BJP’s backing because he is one of chief minister Modi’s confidants and is also very close to L.K. Advani. Shah is the MLA from Farkhez Assembly segment, which is in Advani’s Gandhinagar parliamentary constituency and is the largest in terms of population in the state.

Sohrabuddin, a small-time extortionist, and his wife Kauserbibi were pulled out of a bus and shot dead on the outskirts of Ahmedabad in November 2005. At that time, Gujarat’s anti-terror squad, headed by D.G. Vanzara, had claimed Sohrabuddin was a terrorist who planned to assassinate Modi.

The CBI, according to a television report, has mentioned in today’s chargesheet that Sohrabuddin was killed because he had threatened the marble lobby in the state.

In 2007, the Gujarat government admitted in court that Sohrabuddin and Kauserbi had been wrongly killed. Some of the state’s senior policemen are in jail in connection with the case, including Rajkumar Pandian and Vanzara. The CBI has phone records showing that these policemen were in close and constant touch with Shah.

The case was handed to the CBI by the apex court, which was unhappy with the CID’s tardy rate of investigations.