According to Lyon Mag, whose reporters filmed the incident, the young man who threw the object made a gesture of protest and shouted "vive la révolution". He can then be seen being placed in handcuffs by security services.
Lyon Mag also report that Mr Macron asked his team if he could meet the young man responsible for the incident to understand his motivations.
The president had been attending Sirha Lyon, a meeting of food service and hospitality leaders in the south-eastern city.
There he made a series of policy announcements aimed at trying to revive the restaurant and hotel industries, including a tax exemption for tips paid on bank cards.
Mr Macron also announced the creation of a new “centre of excellence” to promote French culinary traditions and train future chefs.
The incident is not the first time Mr Macron has been accosted by a member of the public.
In June, the president was slapped by a man who leaned across a metal barrier to strike him while shouting “down with Macronism” in Drôme.
Damien Tarel served three months in prison for assaulting a public official.
The incident comes just months before France heads to the polls for a presidential election. Although Mr Macron will not announce his candidacy until next year, he is likely to be battling for re-election until April.
Others, including Brexit negotiator Michel Barnier and National Rally leader Marine Le Pen, have already announced their candidacy.
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