In a handover ceremony, Philippe said his main focus would be to ensure "the highest security level" in the country.
"We live in difficult times with threats abroad and sometimes on our territory ... It's our role to be up to the task", he said, AP reported.
Philippe is in charge until a successor to Gerard Collomb, until recently one of Macron's closest political allies, is appointed. Macron accepted Collomb's resignation late Tuesday, after initially refusing it the previous day. Collomb insisted he wanted to leave to be able to run for mayor of the city of Lyon in 2020.
Collomb, 71, said he regretted leaving the ministry, listing the changes he led over 16 months including passing a counter-terrorism law last year that replaced the state of emergency declared following Nov. 2015 attacks in Paris.
His departure against the president's will leaves the government weakened at a moment when Macron is about to launch sensitive economic reforms.
Macron has pledged to pursue labor changes in the coming months, make changes to unemployment benefits and streamline the pension system.
The leader has had to contend with a series of recent challenges and his popularity has dropped to a record low since his election in May 2017.
Last month, popular environment minister Nicolas Hulot, a former TV personality, unexpectedly announced his resignation on the radio. He explained he felt powerless to hasten the slow progress on green issues.
Macron also struggled for weeks to cope with a major scandal over his former security aide that erupted in July when the man was identified in a video acting violently toward a protester while wearing police equipment.