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For a second day Opposition leaders questioned Mr Key's oversight of the GCSB, which spied illegally on Dotcom.
Responding to Labour leader David Shearer, Mr Key said he was unsure whether domestic spying agency the SIS, for which he is also responsible, or the National Assessments Bureau, were involved in the Dotcom case.
He did not know whether the Department of the Prime Minister and Cabinet (DPMC) was involved.
The DPMC includes intelligence gathering and co-ordination bodies the National Assessments Bureau, the Intelligence Co-ordination Group and the Security & Risk Group. All three organisations could be expected to have been aware of Dotcom.
But Mr Key did not know whether any of the agencies had provided him with any advice about the Dotcom case before the GCSB informed him of its unlawful spying on September 24.
Mr Key appeared to become confused when asked by NZ First leader Winston Peters when his chief of staff was first told of the Ministerial Certificate issued in Mr Key's absence last month by his deputy Bill English.
Mr English issued the certificate to prevent details of the GCSB's involvement in the Dotcom case emerging in court.
"I do not exactly know, but to the best of my knowledge it was on Monday the 17th when I knew," Mr Key said. He later returned to the House and made a personal statement saying it was only this week that he learned of the document.
Labour deputy leader Grant Robertson last night said Mr Key "looked incredibly uncertain" in answering questions about the involvement in the Dotcom case by organisations of which he had oversight.