A terrace for crops, a long road and an 800-metre (2,600 feet) long wall was also found under the waters of the lake, sited in the Andes mountains between Bolivia and Peru.
A terrace for crops, a long road and an 800-metre (2,600 feet) long wall was also found under the waters of the lake, sited in the Andes mountains between Bolivia and Peru.
Dating back 1,000 to 1,500 years ago, the ruins are pre-Incan.
They have been attributed to the indigenous Tiwanaku or Tiahuanaco people, said Lorenzo Epis, the Italian scientist leading the Atahuallpa 2000 scientific expedition.
The holy temple measures 200m by 50m (660ft by 160ft) almost twice the size of an average football pitch.
More than 200 dives were made into the lake, to depths of as much as 30m (100ft), to record the ruins on film.
The explorers found the temple after following a submerged road, in an area of the lake not far from Copacabana town.
The complete findings of the 30-member team, backed by the scientific group Akakor Geographical Exploring, are to be published in November.
The team also hopes to eventually raise the archaeological remains to the surface.
Legends of lost city
The lake has long drawn fascination with various legends around it, including one of an underwater city called Wanaku and another of Inca gold lost by the Spanish.
Stories of the lost treasure were enough to draw the famous French oceanographer Jacques Cousteau to explore the lake. However, he discovered only ancient pottery.
National Geographic also launched an expedition in 1988.
The Tiahuanaco culture lived on the shores of the lake before becoming part of the Incan empire, based in Cusco, Peru.
The Bolivian Government has said it will provide financial and technical support to preserve the ruins.
"This means our civilisations have left more footprints than we had thought," said Antonio Eguino, Bolivia's vice-minister of culture.