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.
But his financial condition deteriorated when the cloth factory shut down and that affected his marital status which eventually resulted into a divorce, the officer stated.
Khan then decided to return India and ISI agents got in touch with him and asked him to work for the agency, he said.
"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.
In fact, Khan's cell phone has also been checked "thoroughly" to establish his other ISI-links and net his accomplices in India, the officer said.
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.
"High-quality FICN (fake Indian currency notes) seized from him may have been brought in from across the border with Nepal and we are looking for those who have helped him in bringing FICN here. There are at least six to seven persons involved with Khan," the STF source said.
The police was also investigating if Khan had gone to Pakistan in the 80s and returned to the city in 2008 after undergoing training there.
Earlier, a city court remanded 51-year-old Khan in police custody for 14 days.
The Special Task Force unit of Kolkata Police had yesterday arrested Khan from the central part of the city for his alleged links with Pakistan's ISI.
Khan has been booked under IPC sections 120B (criminal conspiracy), 121 (waging or attempting to wage war or abetting waging of war against the Government of India), 121A (conspiracy to commit offences punishable by section 121), 122 (collecting arms etc with intention of waging war against the Government of India), 489B (using as genuine forged or counterfeit currency notes or bank notes) and 489C (possession of forged or counterfeit currency-notes or bank-notes).
Meanwhile, a brother of Khan alleged that he was being framed by the police and claimed he was not involved in any kind of illegal activity.
"He was missing since November 7 and we had lodged a missing complaint with the Tiljala Police Station three days later on November 10. We think he was picked up by the police which prepared all fake documents against Khan...This is a conspiracy," he alleged.