"I have asked the government to take the necessary steps so that the use of glysophate can be forbidden as soon as alternatives have been found and at the latest in three years," Macron tweeted a few hours after the committee's surprise decision to extend authorisation for five years.
Frnace as among the nine countries that opposed the move, arguing for a three-year extension and speedy end to the chemicals use because of fear that it is carcinogenic.
Prime Minister Edouard Philippe's office said it "regrets this result" and intends to push for further European-level studies on the product's potential dangers and possible alternatives.
Efforts to find substitutes are already underway in France, Research Minister Frédérique Vidal said.
Evaluation procedures challenged
The French government has asked the European Commission to "rapidly" draw up new evaluation procedures, strengthening their "transparency and independence", Philippe's office said.
Current procedures have come under fire after it became clear that investigations are based on documents supplied by companies seeking licences to sell in the EU.
The Glyphosate Working Group, of which Monsanto is a member, called the decision to extend for five years, instead of the 10 years initially proposed by the Commission, a "triump of politics over science", warning that it would put European agriculture at a competitive disadvantage.
Germany's Bayer company, which is also a member of the group, declared that it regretted the five-year limit.
French big farmers' union, the FNSEA, complained of the government's role in trying to reduce authorisation.
Many farmers appreciate Roundup's effectiveness and low cost.
Along with sulphur, Glyphosate is the most used crop-protection product in the country.