The "private" meeting was held at the Italian premier's request, Macron said after his talks with Pope Francis at the Vatican on Tuesday.
Macron said he had kept his meeting with Conte secret up until now out of respect for Vatican protocol.
"When one visits the pope, it is important that it is not confused with a visit to the Italian government," he commented.
Macron and Conte are said to have enjoyed a dinner at Casina Valadier, a sophisticated restaurant in the capital’s Borghese Gardens, and discussed a range of issues.
The meeting between the two leaders seems to have eased some of the tensions between France and Italy which boiled over during the standoff over the Aquarius, a French migrant rescue ship which was denied entry by Italy and Malta.
France responded to the incident by calling Italy's actions "irresponsible" and Rome retaliated by saying that its neighbours were being “hypocrites”.
With AFP
