The indictment also provided new evidence that the Indian agent - who is not named - ordered the murder of Hardeep Singh Nijjar, a Sikh activist who was shot dead outside a Sikh temple in British Columbia in June.
The Canadian prime minister, Justin Trudeau, said in September there were "credible allegations" that agents of the Indian government had carried out the assassination of Nijjar.
The allegations were denied by India, which called the claims "absurd" and politically motivated.
The US indictment appears to confirm, however, evidence of a global plot allegedly orchestrated in India to silence and kill outspoken critics of the Indian government who support the creation of an independent Sikh state. The Department of Justice has not named the Indian government official - whom it refers to as CC-1 in the indictment and says previously served in India's Central Reserve police force.
It has charged another individual, Nikhil Gupta, 52, of working with the Indian agent. Gupta, an Indian national, is described as a "close associate" of CC-1, and has allegedly described his involvement in international drug and weapons trafficking.
He was arrested and detained on 30 June in the Czech Republic and is being extradited to the US.
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Maresca 'happy' but Chelsea streak ends
The immediate aim of the Friedkin Group is to restore stability to Everton after their takeover on Thursday. In some ways, Sean Dyche has beaten his new employers to it. High-flying Chelsea became the latest team to run into a royal blue wall and out of ideas as they lost valuable ground in the title race.
The Sphinx's plot Will new Royal Mail owner sell off valuable properties?
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Political football
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Theory of nothing earns Saints and Rusk worthy draw
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Semenyo shatters United to leave Amorim facing squall
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Burke helps Saracens show title ambitions
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Pereira's Wolves reign gets off to flying start
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Díaz and Salah double up in leaders' statement win
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