The diplomat was told to leave Moscow amid growing tensions between Russia and the EU over the poisoning of former Russian spy Sergei Skripal and his daughter Yulia in the UK.
The expulsion has been seen as an act of retaliation after the Irish government this week ordered a Russian diplomat based in the embassy in Dublin to leave.
Ireland was just one of 23 countries who received orders to send officials home yesterday.
Ambassadors were called to the Russian foreign ministry yesterday to be told that 59 diplomats were being expelled.
Diplomats from Germany, Italy, Poland, Finland, and the UK are among those who have all been ordered to leave. The Kremlin has also expelled 60 diplomats from the US.
A spokesman for Tánaiste and Foreign Affairs Minister Simon Coveney said there was “no justification” for the expulsion of the Irish official.
“Our staff do not engage in activities which are incompatible with their diplomatic status,” he said. “This decision to expel an Irish diplomat is regrettable.”
The tit-for-tat series of expulsions follows the decision of the Government to order one Russian diplomat to leave this country in the wake of the Salisbury poisoning.
Expelling the official on Tuesday, Mr Coveney said Ireland had an “obligation to act” and to “send out a clear signal” that the attack on Mr Skripal and his daughter was unacceptable.
Taoiseach Leo Varadkar said the Government had taken the decision to expel one Russian diplomat “based on intelligence and advice from Garda intelligence and Defence Forces intelligence”.
“When it comes to terrorism, assassinations, the use of chemical weapons and cyber-terrorism, we are not neutral one bit,” said Mr Varadkar. “We are joined with other neutral countries including Finland and Sweden, who have taken the same course of action as us, in expelling diplomats.
However, after the formal notification was issued, Russia’s ambassador to Ireland, Yury Filatov, said the action was “uncalled for, senseless and regrettable”.
He warned that Ireland’s “unfriendly act” would not go unanswered.
Britain has blamed Russia for the Salisbury poisoning which used a nerve agent. British prime minister Theresa May briefed her European counterparts on the attack during the last European Council meeting, after which a large number of countries decided to expel Russian diplomats.
The EU also recalled its ambassador from Moscow.