Military publication Janes reported Moscow was seeking permission from Jakarta for Russian Aerospace Forces aircraft to be based at the Manuhua Air Force Base at Biak Numfor - about 1400 kilometres from Australia's mainland.
Mr Marles on Tuesday evening said he had spoken with his Indonesian counterpart Sjafrie Sjamsoeddin, who assured him that would not be the case.
"He has said to me in the clearest possible terms, reports of the prospect of Russian aircraft operating from Indonesia are simply not true," Mr Marles said in a statement.
The article caused alarm in Canberra, and prompted Australia's leaders to come out against the proposal, warning Moscow it was not welcome.
Prime Minister Anthony Albanese earlier said the government did not want to "see Russian influence in our region".
"We stand with Ukraine to regard Vladimir Putin as an authoritarian leader who has broken international law, who's attacking the sovereignty of the nation of Ukraine," he told reporters in Melbourne.
In response to the report, Opposition Leader Peter Dutton labelled the Russian president a "murderous dictator" and said he was not welcome in Australia's neighbourhood.
"My message to President Putin is that we don't share any values ... and we do not want the military presence from Russia in our region, which would be destabilising for Southeast Asia," he said.
"It would certainly be a very different calculation for the risks that posed to our country in a period that is very uncertain."
Mr Dutton said it would be "a catastrophic failure" for the Albanese government if it had been unaware of the request.
Russia, which has a "no-limits friendship" with China, has taken steps to strengthen its defence ties with Indonesia as its war on Ukraine dragged into the fourth year.
Russian deputy trade and industry minister Alexey Gruzdev addressed a business forum held in Jakarta on Monday, stressing Moscow's commitment to boosting co-operation.
The deepening defence relationship between Moscow and Jakarta has concerned Canberra.
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