The environment ministry said the country emitted 463 tons of greenhouse gases, measured as carbon dioxide equivalents, or 3.6 percent more than its goal.
It attributed the slip in part to lower oil prices which can prompt people and businesses to consume more in areas such as transportation or heating.
But emissions were down 15.3 percent from 1990 levels.
As part of the Paris climate accord signed by 195 nations in 2015, France has pledged to cut carbon emissions 27 percent from 2013 levels by 2028, and by 75 percent by 2050.
But the disappointing 2016 results show that "France can't be looking down" on other nations, environment minister Nicolas Hulot said.
"So stronger measures seem necessary to remain on track with our targets", he said.
Macron hosted world leaders last month for talks on financing efforts to combat climate change, with a coalition of 225 companies announcing a five-year plan for monitoring 100 of the world's largest corporate greenhouse gas emitters.
"We're not moving fast enough, that's the problem," Macron told the One Planet Summit, called to bolster the 2015 accord in light of US President Donald Trump's decision to pull out of the deal.