The photo of the two leaders sitting six metres apart has sparked much debate online.
French President Emmanuel Macron refused to take a Russian COVID-19 test before his meeting with Vladimir Putin, according to the Kremlin.
Macron was separated from the Russian President by a long table during lengthy discussions over the Ukraine crisis.
The unusual image of the two socially-distanced leaders on Monday has sparked much debate online.
Some had suggested that it was an indication of Putin's cold attitude to his French counterpart, given that he was pictured seated closer to other world leaders late in the week.
But Kremlin spokesperson Dimitry Peskov has stated that Macron refused to undergo a PCR test on his arrival in Russia.
"Some people follow their own rules ... But in this case, a health protocol is applied to protect the health of our president and his host," Peskov told reporters on Friday.
"There are no political considerations on this subject," Peskov added, stating that the physical distance between Putin and Macron did not "interfere in any way with the negotiations".
The Elysée Palace has stated that the health protocols imposed by Russia were "neither acceptable nor compatible with the constraints of our agenda".
"We chose the other option proposed by the Russian protocol," the French president's office added.
Health measures have been considerably tightened within the Kremlin since the start of the pandemic, with President Putin regularly sitting several metres away from guests.
But just three days after Macron and Putin's socially-distanced meeting, the Russian leader was pictured shaking hands with Kazakh President Kassym-Jomart Tokayev and sitting at a much closer table.
Macron's trip to Moscow on Monday aimed at easing tensions between Russia and the West over Ukraine.
Russia has massed more than 100,000 troops along its Ukrainian border, prompting concerns that it is preparing to invade. Moscow has denied the allegations.