"I am sorry in front of everyone for the stupid things we do and for not being true to our word," read the apology on the page of the minister, Sergei Belyakov.
The unusual expression of regret was called a "personal opinion" of Belyakov, who has served as deputy economy minister since August 2012.
Belyakov's page said he was "ashamed" of a "harmful" decision extending a measure introduced last year that diverts some money allocated for future pensions to investments by private funds in the economy.
President Vladimir Putin has denied that the money was being confiscated. But Finance Minister Anton Siluanov said the money was used for crisis measures and for developing the Crimean peninsula, which Russia annexed earlier this year.
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Belyakov's Facebook post also suggested divisions within the government over how to react to a contracting economy made worse by Western sanctions over Ukraine, and adherence to Putin's economic promises.
Russia has attempted to reform its cumbersome Soviet-era pension system for years, eventually adopting a system whereby employers paid a levy which was split between the State Pension Fund and private funds picked by employees or their representatives.