The mini-subs have so far made 52 dives. Mikhail Borzin, the vice president of Lake Baikal's preservation foundation, said the second stage will start in spring 2009.
A foundation spokesman said Monday that researchers studying the Siberian lake have discovered boxes containing ammunition dating back to the 1920s.
"Several boxes containing ammunition were found at a depth of around 300 meters," the spokesman said, adding that the mini-submarine dives had taken place in the Listvennichny Bay, in the southern part of the lake, adding that the boxes will be taken to the surface and their contents later examined by weapon specialists.
Last week, the Mir-1 and Mir-2 mini-submarines dived to the bottom of Lake Baikal to search for sacks of gold taken from the Imperial Russian reserves by the White Army's Admiral Alexander Kolchak when fleeing 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 treasures were discovered by the mini-submarines.
A senior researcher at the Institute of History, the Siberian Branch of the Russian Academy of Sciences, Dmitry Simonov said earlier: "Maybe Lake Baikal contains some gold, but it has no relation to the gold reserves of the Russian Empire that were in the hands of Kolchak."
Baikal, called the Sacred Sea by locals for its size and beauty, is the world's oldest and deepest lake, with an age estimated at 25 million years. It holds around 20% of the planet's freshwater and is home to hundreds of unique species of fauna and flora.
The two-year expedition, which started at the end of July, will include around 160 dives in various parts of the lake.