Dr Coleman was briefed by Immigration NZ chief executive Nigel Bickle on October 28, the day before Dotcom was granted residency.
Dr Coleman distanced himself from the decision, saying it was made by officials. He said: "Ministers had absolutely no knowledge of any pending FBI-NZ Police investigation."
Immigration NZ has now issued a statement saying Dr Coleman was told before Dotcom got residency.
An Immigration NZ spokesman said "the general information about the FBI was passed to Mr Bickle who then passed it to the minister".
The spokesman said a detailed briefing containing "classified information" was given to its Intelligence Manager Theo Kuper.
Mr Kuper didn't give the classified briefing to the Immigration NZ officer making the decision but told him of FBI interest in Dotcom because of his Megaupload ownership, the spokesman said.
"This information formed the briefing to the head of Immigration New Zealand, Nigel Bickle, and in turn Mr Bickle's briefing to the then Minister of Immigration, Jonathan Coleman, on 28 October 2010 to tell him under the no surprises policy that residence had been approved in principle."
• Read more: Dotcom: Why wasn't I blocked?
Labour associate security and intelligence spokesman Grant Robertson said Dr Coleman had not been straight with the public.
"It's quite clear the minister has misled here. He was told. I think people want ministers to be upfront. He's deliberately fudged his answer and that's misleading.
"Dr Coleman needs to come clean. We need to see a full explanation of his role."
Dr Coleman's office rejected repeated requests for an interview yesterday. A spokeswoman said he didn't have time because he was heading from Wellington to Auckland to give a speech - and then refused to say where he was speaking.
A spokeswoman for the Prime Minister said: "The Prime Minister has full confidence in Minister Coleman."
It has also emerged Dotcom has been granted the status of "permanent resident" of New Zealand, given to those who have shown "a commitment to living permanently in NZ".
The original investor residence granted in 2010 had a three-year term - and then became "permanent residency" because Dotcom stuck to the conditions of being allowed into New Zealand, Immigration NZ said.
"Unconditional residence can be granted to Investor Plus applicants after three years if they provide INZ with evidence they have continued to meet requirements.
"INZ can confirm that Mr Dotcom met all the requirements of the Investor Plus policy and has been granted unconditional residence."