The culmination of decades of campaigning by separatists, the November 4 vote will see the Pacific archipelago's 174,000 voters choose whether to break from their old colonial master.
Philippe on Tuesday said "it was appropriate that the state be impartial" in helping organise the referendum, responding to calls by the centre-right Republicans party to speak out on the issue.
"This is the line that I set myself when I was appointed, this is the line that was restated by the president during his trip to New Caledonia, and I will not budge from this line because I think it's right," Philippe said.
Ahead of his visit to the capital Noumea in May, President Emmanuel Macron said "it's not up to us to influence this choice," adding that he was hoping to avoid any "unnecessary tensions".
"I respect this vote... It's an example, and the world is watching us," Macron said.
New Caledonia currently holds a unique position as an overseas possession that formulates its own tax, labour laws and trade policy but not defence or foreign policy.
Recent opinion polls have shown that between 60 to 69 percent of New Caledonians support remaining a part of France.
Better known for its stunning lagoons, pristine Pacific beaches and diverse wildlife, the territory is a strategic foothold for France in the Asia Pacific region, but economic inequality has persisted despite efforts to improve living standards for the indigenous Melanesian Kanak population.
It has seen years of bitter political feuding between independence advocates and those who are determined to remain part of France.
Unrest shook the islands in the mid-1980s with as many as 70 people thought to have been killed.
An agreement was signed between France and New Caledonia in 1998 that promised greater autonomy for the archipelago and its Kanak population.
Under the terms of that deal an independence referendum needed to be held by the end of 2018.
After the vote, France will take "a number of initiatives to ensure that the future of New Caledonia is built in good faith," Philippe said.