Gennady Onishchenko, 63, who had been at the helm of the consumer protection agency Rospotrebnadzor since 2004, has been relieved of his duties, the government said late yestesday.
Onishchenko has been appointed as an aide to Prime Minister Dmitry Medvedev, according to a government statement.
His deputy Anna Popova was appointed his temporary replacement.
Under Onishchenko, the consumer protection agency, which enforces sanitary norms, was widely seen as a tool to punish Russia's neighbours for seeking closer ties with the West or other perceived transgressions.
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In July, Onishchenko's watchdog banned chocolates from Ukraine over safety concerns, the measure coming after apparently fruitless talks between President Vladimir Putin and his Ukrainian counterpart Viktor Yanukovych over Kiev's European Union ambitions.
This month Russia criticised the quality of Dutch dairy products and hinted at possible sanctions during a diplomatic row between the two countries.
The government has repeatedly denied banning foreign imports for political reasons. It remains unclear if Onishchenko's dismissal will lead to a change in policy.
Onishchenko even ventured into domestic politics, advising Russians to stay at home during opposition protests against President Vladimir Putin lest they catch cold.