Kolodko adds to a growing list of medal winners caught out in new tests on samples taken in London and at the 2008 Beijing Games.
The IOC said a new test on Kolodko's doping sample had found two banned substances -- the turinabol and the growth hormone ipamorelin.
Kolodko finished third but moved up to the silver medal one week after the competition when the winner Nadzeya Ostapchuk of Belarus was revealed to have failed a test.
The IOC ordered the Russian Olympic Committee to "secure the return to the IOC, as soon as possible, of the medal, the medallist pin and the diploma" given to Kolodko.
Following accusations of 'state-sponsored' doping made against Russia by Canadian lawyer Richard McLaren in an investigation for the World Anti-Doping Agency (WADA), the IOC ordered new tests on hundreds of samples stored since the Beijing and London Games.
It later announced that 98 new failed tests had been uncovered.
The Russian 4x100m women's relay team have lost their Beijing gold medal and the 4x400m team their silver because of failures.
Yulia Chermoshanskaya from the 4x100m failed a doping re-test along with Anastasia Kapachinskaya from the 4x400m.
In each case banned steroids were found.
Russia has been suspended from the International Association of Athletics Federations (IAAF) because of the doping scandal.
With a world athletics championships to be held in London next August, IAAF president Sebastian Coe told AFP on Friday there is "no timeframe" for Russia's return to international competition.
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