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Radio New Zealand reported an Official Information Act request has revealed Immigration New Zealand asked the SIS to investigate the internet tycoon.
The SIS have said they were not involved in the surveillance of Dotcom, but did pass on a request in October last year from the FBI to New Zealand police about carrying out a joint investigation into his activities.
The SIS told Immigration New Zealand two weeks later it had no security concerns.
In September this year the Government Communications Security Bureau (GCSB) admitted it illegally monitored Dotcom after relying on incorrect police information about his residency.
Prime Minister John Key said the SIS and GCSB operated separately.
"These are completely different operations - I mean the GCSB's involvement was at the request of Organised Financial Crime Agency of New Zealand; SIS is part of the general procedures around getting residency class visa," said Mr Key.
Dotcom is fighting extradition to the United States to face charges of internet piracy and fraud.