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India's top court on Friday ordered an autonomous federal anti-corruption commission to quickly complete a probe of two top officials of the country's investigative agency who have been sent on leave amid an internal feud.

The Supreme Court took up a petition by Alok Verma, the director of the Central Bureau of Investigation, who challenged the government for divesting him of powers amid an agency inquiry of his deputy, Rakesh Asthana.

The late night personnel changes on Tuesday are seen as an embarrassment for Prime Minister Narendra Modi's government with the agency's internal feud becoming public.

Three judges ordered India's Central Vigilance Commission, which had recommended the removal of both Verma and Asthana from their posts, to complete the probe within two weeks. They also said that M. Nageswar Rao, whom the government named as interim CBI chief, could not take any major decisions.

Under Verma, the federal agency filed a case against Asthana on allegations that he took bribes from a meat exporter.

Rahul Gandhi, the main opposition Indian National Congress party chief, has accused Modi of removing Verma in order to quash a probe into the purchase of 36 French Rafale aircraft for the Indian air force. Gandhi appears bent on making the aircraft purchase an election issue ahead of national polls due early next year.

On Friday, Gandhi led a protest by his party workers outside the New Delhi office of the CBI, demanding an investigation by a parliamentary panel into the Rafale deal Modi's government signed with the French government in 2016.

Gandhi has accused the government of buying the aircraft at nearly three times the price the Congress party had negotiated before losing power to Modi's Bharatiya Janata Party in 2014. Defense Minister Nirmala Sitharaman has refuted the claim, but declined to disclose the value of the deal, citing a secrecy clause.

Gandhi also accused Modi's government of favoring the company owned by industrialist Anil Ambani, Reliance Group, when choosing an Indian partner for Dassault, the French manufacturer of the Rafale aircraft. India's government has denied any wrongdoing.

Dassault said earlier this month that it has "freely chosen to make a partnership" with India's Reliance Group.