Mikhail Petrakov, who has been ambassador since August, was told by officials that recent threats by Russia to demolish buildings in Ukraine's capital Kyiv were a violation of international law.
A release by the Russian foreign affairs department said the government's patience had been "exhausted" and it would start targeting defence buildings in Kyiv as a result.
"We are notifying foreign citizens, including the personnel of diplomatic missions and international organisations of the need to leave the city as soon as possible.
"We are urging residents of the Ukrainian capital not to approach facilities of the military and administrative infrastructure of the Zelenskiy regime," the release said.
Australia's Foreign Minister Penny Wong said the threats were totally unacceptable and required action.
"(The threats) are a further demonstration of Russia's complete disregard for international law and civilian safety," she said.
"Australia stands steadfast in its support for Ukraine and we call on Russia to end its illegal and immoral invasion."
It is the second time a Russian ambassador to Australia has been hauled in to the Department of Foreign Affairs in as many year.
Mr Petrakov's predecessor was called to give information after Melbourne man Oscar Jenkins was killed fighting for Ukraine in January 2025.
Mr Jenkins was taken into custody by Russian troops and died while detained, sparking outrage and diplomatic action.
In 2014, then-ambassador Vladimir Morozov was summoned to explain Russia's decision to send troops into Crimea.
Australia's diplomatic visits to Russia were suspended as a result.
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