Philippe rejected the committee's recommendations for a reorganisation of the government, calling it a flagrant disregard of the fundamental principles underlying the separation of powers.
"The Senate commission inquiry and the Senate have chosen to deliver a report that is very political," Philippe said in a rare speech outside the Prime minister's building Thursday.
"I am not surprised," he said in reference to the predominantly right-wing Senate, "but I am disappointed."
In a damning 120-page report published on Wednesday, the Senate committee flagged up serious failings within the president's office that had allowed Alexandre Benalla, a former security aide, to acquire excessive powers, including two diplomatic passports.
It suggested also that Benalla's alleged links to a Russian oligarch posed a serious conflict of interest and a potential threat to presidential security and national interests.
Also in its report, the Senate committee put forward a number of recommendations to improve the president's security, starting with better vetting of potential collaborators.
The French Prime minister on Thursday dismissed the Senate's advice.
Overstepping its powers
Philippe said he was "extremely surprised" that some of the recommendations put forward by the committee "concern the presidency and the government – explicitly and exclusively".
He added that "it is not the role of the National Assembly, nor the Senate to decide the internal organisation of the French Republic."
The Senate thinks differently.
"When it comes to the security of the president, it concerns the entire Republic," the authors of the six-month inquiry insisted, dismissing Philippe's accusations that they had overstepped their powers.
"The principles underlying the separation of powers should not be used to stop us from keeping the government in check," senators said.
The members of the commission inquiry insist nonetheless that they "respect the independence of judicial authorities", and that their quizzing Benalla was not an attempt to compete with them.
The Benalla scandal erupted last July, after video footage emerged of the bodyguard punching a protester at a May Day demonstration, at which he was observing a police operation.
The committee concluded Benalla had benefited from "incomprehensible indulgence" from the Elysée when it came to disciplining him for his transgressions.