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The 7.5 metre yacht was last heard from on April 16 when it left Bluff headed for Preservation Inlet at the southwest of the South Island.
Munetra was reported missing to police last Thursday.
Two of the three people on board are German citizens who were visiting New Zealand on a gap year after finishing school. They are Lea Tietz and Veronika Steudler, both aged 19, from the district of Gorlitz in Germany.
The skipper of the yacht is also a German, who has been living in New Zealand for about four years and has been working on a dairy farm in Central Southland. He is Andre Kinzler aged 33.
Police say the families of Ms Tietz and Ms Steudler have been informed of the situation but police working through the German Embassy have not yet been able to make contact with Mr Kinzler's relatives.
Police say they are now working on a missing persons' inquiry in relation to the disappearance of the yacht.
Although they have gathered a lot of good information about the movements of the trio prior to the boat leaving Bluff on 16 April, they are still working to further establish the facts.
Police say they had received no information that suggested any foul play.
Ms Tietz and Ms Steudler had known each other from Germany and had been travelling in New Zealand since September last year, police said.
They had been travelling intermittently together over that time and were both due to go home next month.
Ms Tietz met Mr Kinzler on Stewart Island around a month ago, and indications were that the trip had been planned since then.
Police said Mr Kinzler's sailing experience was also a focus of their inquiries.
"We know that he had purchased the boat within the past 12 months but the information we've gathered to date suggests that his previous sailing experience may have been limited," Inspector Todd said.
Since Thursday a large search and rescue team, including an Air Force Orion, had been scouring the coast of the southern South Island and around Stewart and the Muttonbird Islands, for any sign of the vessel.
The search has included coastline searches by a plane and two helicopters, with an Airforce Orion searching approximately 80,000 square kilometres of ocean. The search area was effectively the width of the South Island to a point 150km south of Stewart Island.
The search is now in a limited continuous search phase, which meant the team would continue to regularly receive and evaluate the latest information supplied from the Rescue Coordination Centre about tidal patterns, current movements and debris already located, to identify potential actions or directions for future searches.
Searchers had also asked local fishermen and boaties operating in the vicinity of the search area to report any new and relevant information to them.