Asked about those suspicions on Monday at a joint news conference with the Russian president in Versailles, Macron said that the subject had not come up during their working lunch - because he had already raised it when Putin called to congratulate him on his victory.
Regarding the conflict in Syria, the French President also had strong words for Russian Federation and its allies, including Syrian leader Bashar al-Assad.
"We disagree on a number of things but at least we discussed them", Macron said.
At the G7 summit in Sicily at the weekend Mr Macron said: "It is essential to talk to Russian Federation because there are a number of worldwide issues that will not be resolved without a tough dialogue with them".
The discussions Monday, however, will be less about building than rebuilding, as both leaders hope to fix a relationship that has recently grown fraught. The two leaders later visited some of its exhibits.
Their first meeting since Macron took office provided another test of the Frenchman's diplomatic skills after his memorable vice-grip handshake last week with US President Donald Trump. "Russia Today and Sputnik were organs of influence and propaganda that spread counterfeit truths about me", he said, while standing next to Putin. That's the first time a French president has done that, says Sacha Koulaeva with the International Federation of Human Rights.
Human Rights Watch said in a new report last week that high-level officials in Russia's Chechnya humiliated inmates during visits to detention facilities where gay people were allegedly held and tortured. Putin had supported Macron's opponent, Marine Le Pen, and received the nationalist at the Kremlin during her campaign. Macron's aides also claimed that Russian groups launched hacking attacks on his campaign.
Russian President Vladimir Putin has arrived in France for talks with newly-elected French President Emmanuel Macron. "Let's tell things like they are: Russia Today and Sputnik didn't behave like organs of the press and journalists, they behaved like organs of influence and mendacious propaganda". That means that we want Assad to go away but not necessarily the regime to change.More news: Apple Announces 10.5-Inch iPad Pro
"It is essential to talk to Russia because there are many worldwide issues that will not be resolved without a tough exchange with the Russians", Macron said at the G7 gathering.
"We are ready to receive any person, always", he said.
"As for me, I will be constantly vigilant on these issues, which are in keeping with our values", Mr Macron said.
The pair discussed the Western sanctions imposed on Russia over its military involvement in Ukraine as well as allegations of Russian meddling in France's election campaign.
Macron's invitation for Putin was a surprise after his tough stance on Russian Federation during the French election.
Nabi Abdullaev, associate director for Russian Federation at the global consultancy Control Risks Group, told the German Press Agency (DPA) the meeting would be mainly symbolic.
BEARDSLEY: News magazine editor Makarian says Macron felt this was something he couldn't forget and he couldn't forgive.
France helped spearhead the sanctions, which have seriously dented EU-Russia trade.