Madhuri Gupta, who had been working in the Indian embassy in Islamabad prior to her arrest, was booked under three sections of the act, Deputy Police Commissioner Shibesh Singh told AFP.
Gupta, 53, worked in the embassys information service. She was called back to New Delhi in April on the pretext of consultations before police swooped on her at home.
Her lawyer, Joginder Dasiya, confirmed that charges had been filed in court.
“When I get the copy tomorrow morning (of the police charges) I will be able to comment. At the moment I have no details,” Dasiya said.
Depending on the precise nature of the charges, Gupta could face a prison sentence of anywhere between three and 14 years if convicted.
According to Indian police, Gupta had been under surveillance for six months before she was taken into custody.
She had worked in the Indian mission for nearly three years and news reports said she was alleged to have passed on information from the Islamabad head of Indias external intelligence service.
Former diplomats said Gupta would in theory have had limited access in her role in the information wing.
As a second secretary, she ranked low in the diplomatic hierarchy, senior only to the entry-level third secretary.
Pakistan had played down the scandal, which broke just days before the prime ministers of India and Pakistan met for talks at a South Asian leadership summit in Bhutan.
Soon after the arrest, Gupta's lawyer had insisted that her client was being framed and said police had failed to provide any evidence against her.
A Delhi court had refused Dahiya's arguments for bail, saying the alleged crimes were “too grave” in nature.