The 56 year-old was seen boarding the Mir-1 submarine before being hoisted into the water to begin his journey into the lake, which is also known as the 'Blue Eye of Siberia', and contains more water than all of the North American Great Lakes combined, the AAP reported.
Putin was reportedly delighted with his journey and said, "The dive is going perfectly, there is a perfect view with the lights."
He, however, expressed some surprise about how murky the water was in the lake, which contains around a fifth of the world's freshwater reserves.
"The water of course is clean from an ecological point of view but in fact it's a plankton soup, or so I called it," he said.
The Mir-1 had earlier set a world record in 2008 for the deepest dive in a lake by diving to 1,680 metres (5,512 feet).
According to reports, Putin in his daring expedition dived to a depth of around 1,400 metres (4,600 feet).
The Russian Prime Minister is famous for indulging in numerous voyages and prides himself on keeping a remarkable physical condition, and has raised eyebrows with a series of highly publicized stunts over the past couple of years.
Earlier, Putin had clipped a radio transmitter onto a beluga whale named Dasha in Russia's Far East.