French Health Minister Agnès Buzyn said the refunds paid by French social security – currently 30 percent of the treatment – will be phased down to 15 percent in 2020 and then to zero in 2021.
"I have decided to start the process for complete non-reimbursement," Buzyn told the Le Parisien daily newspaper, adding that she was following the advice of the French National Authority for Health (HAS).
She added that the transition period would allow both patients and pharmaceutical companies to adapt to the new system.
The HAS at the end of June published a damning scientific view, saying that homeopathy had "not demonstrated scientifically a sufficient effectiveness to justify a reimbursement".
Buzyn acknowledged that the move could prove unpopular and emphasised it should not stop doctors prescribing homeopathic medicines or patients from buying them.
French company Boiron, the world leader in homeopathic products, denounced what it said was an "incomprehensible and incoherent decision".
The company asked for an urgent meeting with President Emmanuel Macron and said it would "do everything to fight" the decision.