Cybersecurity analysts quickly detected Russian fingerprints behind the hacking of the Macron campaign's emails and internal communications earlier this month.
The Kremlin has denied involvement, and Putin today reiterated that Russia never meddled in the French election. He did, however, defend his decision to receive the pro-Russian Le Pen in Moscow in late March, one month before the first vote in the two-round French election.
Putin told reporters that Macron had not broached the subject of the cyberattack in their talks.
"We are quite capable of trying to move forward together in terms of the so-called Russian interference in the elections," Putin told a news conference, in response to a question. "The issue has not been raised. The French President did not show any interest, and I even less."
But Macron did show more than a little interest in the topic, especially when asked by a Russian journalist why it had been so difficult for certain reporters to get access to his campaign headquarters during the election.
"I have always had an exemplary relationship with foreign journalists, but they have to be journalists. Russia Today and Sputnik were organs of influence and propaganda that spread counterfeit truths about me," he replied, referring to the Russian TV network and news agency.
Both media outlets are controlled by the Russian Government.
"It is not for me to comment on Madame Le Pen's visit" to Moscow, Macron said, in response to another question about the vote. "Elections are the decisions of sovereign people."
The presidents' meeting at the 17th-century Chateau de Versailles, one of Europe's most opulent royal palaces, came at a time when relations between Paris and Moscow have reached one of their lowest points in decades, mostly because of the war in Syria.
France has been highly critical of Syrian President Bashar al-Assad, whom the Kremlin has backed for years. Last year, Putin abruptly cancelled a visit to France after Macron's predecessor, François Hollande, decried Russian bombings in the Syrian city of Aleppo as a "war crime".
Macron said today that the use of chemical weapons in Syria constituted a "red line" for France and "would result in reprisals and an immediate response, at least where France is concerned". Syria has been accused of using chemical weapons, including chlorine gas and much-deadlier nerve agents, during the conflict.
Trump last month ordered a missile attack on a Syrian air base in response to a chemical attack in Idlib province that killed nearly 100 people. Russia protested that the US retaliation violated international law and said it would ruin bilateral relations.
US President Barack Obama had also pledged strong action against Syria if it crossed a "red line" by using chemical weapons. But a year later, in 2013, Obama was widely criticised for holding off on military action against Syria when he failed to get congressional approval for a strike in the wake of a chemical-weapons attack. The US Government subsequently worked with Russia on a deal that was supposed to rid Syria of such weapons.
France and Russia are also divided over the Putin Administration's support for pro-Russian rebels in eastern Ukraine and Russia's annexation of Crimea in 2014, which led to the imposition of sanctions by Europe and the United States.
Macron said France and Russia would pursue further dialogue in the "Normandy" format, including France, Germany, Russia and Ukraine.
Standing next to his Russian counterpart, France's new President also pledged to defend "all people, all minorities". He explicitly mentioned workers employed at Western-backed nonprofit groups in Russia - who are often tagged "foreign agents" by the Russian government - and the reported abuse of gay people by authorities in Chechnya.
"I will be constantly vigilant on these issues," Macron said.
Macron showed Putin around an exhibition commemorating Russian Tsar Peter the Great, who visited France in 1717.
Macron had name-checked Putin in an interview this weekend, suggesting that he knew how to deal with such leaders.
"Donald Trump, the Turkish President or the Russian President are in a balance-of-power logic, which doesn't bother me," Macron said. "I don't believe in the diplomacy of public invective, but in my bilateral conversations, I will let nothing pass. That's how you make yourself respected."