The watchdog said in a statement that a ban on flower deliveries from the Netherlands -- a country that prides itself on its tulips -- was "highly probable."
The statement said that Dutch flowers could be banned because the harmful organisms they contain "pose a serious threat to the country's economy and agricultural production."
According to data published by news site Gazeta.Ru, Dutch flowers could suffer tens of millions of dollars in losses.
The West has accused the separatist insurgency of eastern Ukraine of shooting down the plane using a missile supplied by Russia.
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Moscow has repeatedly denied any involvement in the incident, accusing the Ukrainian military instead.
Russia has staunchly opposed the creation of a tribunal to prosecute those responsible for the downing of MH17.
Yesterday, the country introduced an alternative draft resolution at the UN Security Council in an attempt to thwart the initiative put forth by Malaysia.
On the first anniversary of the tragedy last week, Russian Foreign Minister Sergei Lavrov laid a basket of flowers outside the Dutch embassy in Moscow.
Last August, Russia banned the import of meat, dairy and produce from European Union member states and other Western countries in retaliation for sanctions imposed on Moscow over the Ukraine crisis.
President Vladimir Putin last month ordered that the embargo be maintained until June of next year.