"I am resigning as [Nashi] federal commissar," Yakemenko said speaking at the group's congress. Yakemenko will now head a committee on youth affairs at the Science and Education Ministry.
Nikita Borovikov, 26, was elected to replace Yakemenko in July, when some 10,000 Nashi activists and supporters gathered on Lake Seliger, a popular resort in western Russia. The gathering was briefly attended by First Deputy Prime Minister Dmitry Medvedev.
The outgoing leader praised the group's contribution to reviving patriotic sentiments among fellow Russians and noted the emergence of successful business executives from among its activists.
Nashi, founded in March 2005, has been involved in activities like a recent blockade of Estonia's Embassy in Moscow in response to the ex-Soviet Baltic state's decision to move a Soviet-era war monument in the capital, Tallinn.
The group also held rallies to garner support for United Russia party backed by President Vladimir Putin in the run-up to the December 2 parliamentary polls.
Responding earlier to accusations of radicalism within the group, Medvedev, who Putin recently backed as his successor, said there was no reason to fear Nashi.
Medvedev said authorities should welcome youth organizations whose efforts unite young people after a period of anarchy that ensued the collapse of the Soviet Union.