The Commission said: "We have taken into account the latest state of scientific research" and will "work with the member states to find a solution that enjoys the largest possible support."
No date has yet been set for when discussions with representatives of EU member states will start.
EU Commissioner for Health and Food Safety Vytenis Andriukaitis said politics should not outweigh science in the debate over glyphosate: "I must be humble, I am not a scientific expert, but it seems to me that political opinions cannot outweigh broadly agreed scientific opinions.
"As a doctor, I rely on science. Therefore, I will continue to base my decisions on science and on the rule of law.
"I will also continue to work on sustainable EU food policy that promotes innovation, technological advancements and strives to respect environment while providing EU citizens with safe and nutritious food at affordable prices…I invite all MEPs to be my allies in this endeavor."
This decision by the Commission follows up on a March 2017 conclusion by the European Chemicals Agency (ECHA) that the available scientific evidence did not meet the criteria to classify glyphosate as a carcinogen, as a mutagen or as toxic for reproduction.
The same conclusion was also reached by the European Food Safety Authority.