In 2008 a similar vault was created in Norway, but the new facility in northern Siberia is the only one of its kind that solely uses the unique natural permafrost cooling system.
There is already a small unit containing 100,000 samples on the site, in the Sakha Republic, but a new purpose-built extension will turn it into the largest anywhere on the planet.
Georgy Kuzmin, lead researcher of the Permafrost Institute - part of the Siberian Branch of the Russian Academy of Sciences - said: 'The project does not use any machinery or electricity or gas.
'It only uses natural cold and, respectively, the operating costs are minimal.'
The first part of the cryostorage facility in Yakutsk was opened in December 2012, some 35 years after Soviet scientists began an experiment in a mine at the Permafrost Institute.
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There is already a small unit containing 100,000 samples on the site, but a new extension will mean many more seeds can be stored
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The vault will be able to accommodate 1.5million seed samples, and will be filled with collections from Russia and the rest of the world
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Scientists in Siberia will be able to keep a stockpile of common seeds for up to 100 years without needing to replant them
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Temperatures in Yakutsk's permafrost caves are so low that quirky ice sculptures like this office scene this can be made
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Yakutsk has an average winter temperature of -34C, making it the coldest major city in the world
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Brrr-ight idea: The vault is in Yakutsk, the coldest city on the planet - which is more than 3,000 miles from the Russian capital Moscow
At a depth of 12 metres they began the long-term storage of seeds from legumes at a temperature of about -7C using just the natural cold from permafrost.
Scientists were able to prove that seeds can be stored at that temperature, rather than colder, without losing any of their germinating capacity.
Later, about 1,000 seeds from crops common in the Sakha Republic, also known as Yakutia, were added to the vault along with some endemic, rare and endangered plant species.
By the time the new facility opened in 2012, there were 11,000 samples and there is now currently space for about 100,000 seeds from around Russia.
The unique building does not use any fans or pumps to keep the temperature under the ground cool and instead simply relies on the natural cold air.
The new phase will be able to accommodate 1.5million seed samples, and will be filled with collections from Russia and the rest of the world.
Scientists aim to preserve many of the most endangered species of plants as well as keep a stockpile of common seeds for up to 100 years that they won't need to replant.
They will be placed inside special sealed glass containers, with the freezing temperatures outside preserving them in a giant natural refrigerator.
There is a similar storage laboratory in Svalbard, in Norway, but it relies upon artificial cooling measures as well as permafrost to lower temperatures to -18 degrees Celsius.
This, according to scientists in Siberia, makes it less safe because of the dangers of a power outage posing a risk to the ability to keep the facility cool.
Global warming may also raise the temperatures of the Norwegian ice fields and melt the permafrost, something that is not possible in the Sakha Republic.
Nikolai Goncharov, from the Institute of Cytology and Genetics in Novosibirsk, said: 'When global temperatures get warmer by five degrees, the glaciers on Svalbard will melt.
'To melt the permafrost in Yakutia temperatures need to rise by about 20 degrees.
'So we have quite a unique situation in which the permafrost can create storage in natural conditions that will keep the desired temperature.
'It is an eternal, and environmentally-friendly, system that cannot be affected by any disasters.'
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