About 18 people including police officers and security dressed in plain clothing were also gathered outside the reception area.
Five Eyes has almost a 70-year history and is a spying partnership of the United States, Australia, Canada, the United Kingdom and New Zealand.
And the security presence has sent locals into a flurry in the southern tourist hotspot.
A staff member at Betty's Liquor Store along Arrowtown's main drag, who did not wish to be named, reported seeing what he described as "snipers" on Thursday evening.
"I saw some snipers just beside the trees, hidden, as I was passing through to Queenstown," he said.
"I saw only two, there might be more . . . with guns. Maybe snipers or like rifles."
Other shopkeepers in the town reported seeing bodyguards roaming the streets on Wednesday afternoon.
The security operation, centred around Arrowtown, is expected to continue for about a week.
Word on the street among locals was that the conference was taking place at Millbrook Resort.
Millbrook Resort has a 27-hole golf course, an activity the Otago Daily Times reported would feature on the visitor's itinerary.
The Herald have contacted management for comment.
MP for Clutha-Southland Todd Barclay was in Arrowtown for the Autumn Festival today.
In between judging the village scarecrow competition and talking to locals he said he didn't know much about "why they are here or what they are doing here".
"Otago and Southland are pretty used to having reasonably high profile visitors here. The nature of the background of some of the visitors who are here at the moment is probably leading to some intrigue," he said.
"Any high profile visitors that come to our country whether politicians, spies or famous actresses and actors, they all contribute to the profile of our tourism proposition."
Tongues wagged this week about the "very, very important person" expected to touch down in Arrowtown, with Barack Obama and Bill Gates' names dropped in the mix.
Speculation was sparked after the ODT reported a major security operation dubbed Operation Silver Fern, had led to beefed up security in the town, set to include armed members of the police special tactics group and more than a dozen staff from Christchurch.
However, Prime Minister Bill English's office ruled out a current or former head of state on Thursday.
"The Government is hosting a conference with a number of senior officials from overseas.
"Due to specific security requirements we cannot comment further at this time. However, as police have pointed out they are not aware of a visit to Queenstown by a current or former head of state."
It is believed that Federal Bureau of Investigation director James Comey and Central Intelligence Agency director Mike Pompeo are among members, from about 15 agencies, attending the conference.
It is not known which government ministers are attending the Queenstown conference.
Police Minister Paula Bennett is on holiday and will not be attending and Minister of Foreign Affairs Murray McCully has confirmed he will not be present.
Minister for the GCSB and Security Intelligence Service Chris Finlayson's office could not immediately comment.
Five Eyes was established at the end of World War II for the purpose of sharing intelligence, particularly signals intelligence - the interception of private phone calls, emails and internet chats - globally.
In 2013, US whistleblower Edward Snowden shared a series of documents shedding light on New Zealand's contribution to the alliance, which included spying on a surprising array of our country's friends, trading partners and close Pacific neighbours. These countries' communications are then supplied directly to the US National Security Agency and other Five Eyes agencies.
