Talking about their investigation, the STF officer said that the documents, unearthed from the Collin Street residence of the Khan showed his "deep-rooted" links with the Pakistani agency.
According to him Khan went to Pakistan in 1985 and managed a job at a cloth factory at a monthly salary of Rs 10,000 in Pakistani currency with the help of one of his uncles who is a Pakistani.
"Later on he (Khan) got married to a local woman which helped him getting a Pakistani passport," the officer told PTI.
Khan then decided to return India and ISI agents got in touch with him and asked him to work for the agency, he said.
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"They trained him in code management... There he learnt coding and decoding," the officer said adding that several email address leading to ISI agents were found in Khan's mail.
"He then returned to India in 2008 crossing the Nepal border and started living at 76/B Collin Street in the southern part of the city.
According to another highly-placed STF-source, during the preliminary investigation, it had emerged that Khan alias Mohammed Javed alias Raju was also staying at another address at 15, Topsia Road.
STF was conducting searches in and around the city for Khan's accomplices.