It is believed to have taken a couple of hours for the alarm to be raised after one of the boat's occupants managed to swim ashore and went for help, as his two companions were missing.
However, a second person had also made it to shore and a third person was found dead.
Snr Sgt Pine said a search and rescue operation was launched using a Southern Lakes helicopter and boats on the lake.
Search and Rescue personnel came from Te Anau, with further support provided by police highway patrol officers.
Sen Sgt Pine said given the circumstances, including cold lake water conditions, it was fortunate there had not been further loss of life.
More details, including about safety equipment carried on the boat and how the initial alert was notified, were not immediately available last night.
Police were continuing inquiries and would be investigating on behalf of the coroner, he said.
The Mavora Lakes are accessed from State Highway 94 between Te Anau and Mossburn. There are two lakes, the north, which is a popular boating lake, and the south.
The lakes are part of Te Wahipounamu/southwest New Zealand World Heritage Area.