The weedkiller, introduced in the 1970s by US agro-giant Monsanto under the brand name Roundup, is suspected by some scientists of causing cancer, with a 2015 WHO (World Health Organisation) study determining it was "probably carcinogenic".
Last November, a majority of EU member states voted to renew the licence for the product for five years, rebuking French efforts to limit the approval to just three years pending.
"The president's commitment to forbidding glyphosate within three years is clear," government spokesman Benjamin Griveaux told France Info radio Tuesday.
"We have said that we are going to work with everyone involved, that we will charge the INRA (National Agriculture Research Institute) with finding alternative solutions for glyphosate," he said.
Senators rejected late Monday amendments that would have given the pledge the force of law, though Griveaux rejected claims the government was ceding to pressure from farm lobbies.
"Have a little bit of confidence, don't always think that constraints, sanctions are the only ways of pursuing efficient public policies," he said.
"(Environment Minister) Nicolas Hulot is working with all players and with INRA, and if we find industrial and scientific solutions allowing France to stop using glyphosate in three years, then everyone will have won," he added.