Grassroots members of centrist La Republique en Marche party have made their anger and disappointment clear to the 39-year-old French President, the Financial Times reports.
Mr Macron, who was elected in May, promised his followers that the new party would be a “bottom-up” movement, giving rank and file members a say in how it is run.
But now Mr Macron has been accused of a stitch-up as Christophe Castaner, a minister in his government, is the only candidate in the race.
He will reportedly be elected by a “show of hands” in a secret meeting of just 200 randomly-selected members.
Mr Macron’s supporters, many of whom have been with him since the beginning, fear a betrayal of his pledge to modernise French politics.
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Some have even said they now feel that he “used” them as a tool in his attempts to seize power.
Michel Coste, a former local party boss in the rural region of Ardeche, in southern France, dramatically announced that he would quit the party because decisions were coming “from the top” and that “trust had been broken”.
Mr Macron’s decision to keep Mr Castaner in his government while he runs his party has also led to cries of foul play and conflicts of interest.
Mr Castaner, a former Socialist mayor and regional councillor, was picked over another Macron loyalist, Benjamin Griveaux, partly because of his experience in local politics.
The French president is already planning future regional elections, looking to take over huge swathes of the country, and wants Mr Castaner to groom a new generation of centrist leaders.
Mr Castaner reportedly wants to run the day-to-day operations of La Republique en Marche with a small team of hand-picked advisors.
But this has been met with several challenges by key members for spots on the party’s ruling executive committee.
Many have called for the new party boss to be selected through a ballot of every single member – but it remains to be seen if Mr Macron will bend to their demands.
Mr Macron, who is married to 64-year-old Brigitte, faces trouble abroad as well as at home – after Brexit Secretary David Davis accused him and German Chancellor of “holding up” EU talks.
He said: “Countries like Denmark, countries like Holland, countries like Italy and Spain, countries like Poland can see the big, big benefits in the future deal that we are talking about.
“Germany and France are the most powerful players on the continent of Europe. Of course they are. What they believe is very influential, sometimes decisively so. But it’s a whole of Europe decision.”
EU bosses continue to play hardball with the UK government, having said it needs to make more concessions before trade talks can even begin.
The charismatic Mr Macron is seen as a key influence on other Eurozone leaders.