The opposition party said in a statement yesterday that two other members of the government, public accounts minister Gerald Darmanin and junior environment minister Sebastien Lecornu, had also been expelled.
Two other MPs who back Macron, Thierry Solere and Franck Riester, were also shown the door for "supporting the presidential majority" and, in some cases, backing candidates running against the Republicans.
Party leaders had been seeking to boot out the Macron supporters for weeks.
Macron swept to power in May, beating far-right leader Marine Le Pen to the presidency just over a year after forming his centrist En Marche (On The Move) party.
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Macron, an ex-investment banker and economy minister in the government of Socialist predecessor Francois Hollande, claims he is neither of the left nor the right and has sought allies in both camps.
Philippe, a former mayor of the port city of Le Havre, was a little-known centre-right MP when Macron named him premier in May.
En Marche and its allies hold 313 seats in the national assembly, while the Republicans grouping holds 100.