The spokesman said the Mir-1 and the Mir-2, which completed the first stage of their study of the world's largest and deepest freshwater lake last week, will be stored at the Irkutsk Aviation Plant.
The mini-subs have made 52 dives since late July. Mikhail Borzin, the vice president of the foundation for the preservation of Lake Baikal, said a number of significant scientific discoveries had been made during the expedition.
Baikal has not been studied completely and many questions still remain unanswered, including the origins of the lake and the unique organisms that live in it.
Scientists estimate Baikal is some 25 million years old. Researchers also took samples of oil that seeps through cracks in the lake's bedrock and is digested by the lake's organisms.
In addition, the mini-subs also searched for sacks of gold taken from the Imperial Russian reserves by the White Army's Admiral Alexander Kolchak before fleeing across the lake from the Bolsheviks in the winter of 1919-1920.
Some of the White Army officers reputedly froze on the ice as temperatures dropped to 60 degrees Celsius below zero, and the gold is thought to have sunk when the spring thaw came. However, no treasure, except boxes containing ammunition dating back to 1920s, was discovered.
The second stage of the expedition will start in the spring of 2009, and a total of 160 deepwater dives are planned over the two years of research.
Lake Baikal, a UNESCO World Heritage site, holds around 20% of the planet's freshwater.