Speculation about the visit was sparked after the Otago Daily Times reported a "very, very important person" was set to arrive in the region and strong security measures were underway in preparation.
The ODT said it was understood the operation would continue for about a week with golf featuring on the itinerary.
Comey has in the centre of several high-profile controversies over the the last five months, firstly when he reopened an investigation into Hillary Clinton's use of a private email server just before the US Presidential election, and more recently when his agency launched an investigation into Russia's influence over the US election.
Visits by the top spies are usually kept under wraps, although former Prime Minister John Key last year disclosed the then US director of intelligence Jim Clapper was in town when asked why a US plane was at the military terminal in Wellington.
Clapper visited on his way to Australia for a Five Eyes conference.
It is not known which Government ministers are attending the Queenstown conference.
Minister for the Government Communications and Security Bureau (GCSB) and Security Intelligence Service (SIS) Chris Finlayson's is expected to attend the conference.
A spokesman for Police Commissioner Mike Bush refused to comment.
Police Minister Paula Bennett is on holiday and will not be attending.
Comey was last in New Zealand in March 2016, when he met with Finlayson and Bush.