Arriving after a three-day trip to Australia, Macron declined to take a position on the independence vote, although during last year's presidential election campaign he expressed a preference for the territory remaining part of France .
The visit was an opportunity to "pay tribute to some important occasions in our common history, occasions which may have sometimes been painful", he said.
Separatist hostage-taking anniversary
Among those painful occasions was the storming of a cave on the island of Ouvéa that saw 21 people killed.
Macron will take part in a ceremony marking the 30th anniversary of the event, in which separatists of the Kanak and Socialist National Liberation Front (FLNKS) killed four gendarmes and took 27 others hostage.
When French commandos stormed the cave 19 separatists and two soldiers were killed.
A year later separatist leaders Jean-Marie Tjibaou and Yeiwéné Yeiwéné were murdered by fellow separatist Djubella Wea at the monument to the Kanaks who were killed.
Some of their relatives and local residents have threatened to disrupt the ceremony, which takes place at a monument commemorating the dead gendarmes, although other Kanak tribes have called on the population to take part in it.
Saturday is the anniversary of the 1998 Nouméa accords, which ended the violence and started a process of decolonisation and increasing autonomy that will culminate in the referendum in November.
Macron will mark the occasion by presenting the local government with the original of France's declaration of its colonisation of the territory in 1853.
Apart from a desire to counter British and Dutch presence in the Pacific, France's main reasons for taking over the territory was to build a penal colony, which later served to imprison left-wing rebels from the 1871 Paris commune and Algerians who fought France's colonisation of their country.
The French president, the seventh to visit New Caledonia but the first to go to Ouvéa, will make what is being billed as a "major speech" at a theatre built on the site of the penal colony.
Loyalists to march for flag
Of the archipelago's 270,000 inhabitants, about 40 percent are indigenous Kanaks, 27 percent of European origin, the rest defining themselves as mixed race or of other origin.
An opinion poll has shown a big majority likely to reject independence in November's vote and some of the loyalist camp has criticised Macron's visit as concentrating too much on Kanak identity.
They have organised a march in honour of the French tricolore flag on Friday, supported by three organisations, including the far-right National Front.Local representatives of the mainstream right Republicans will also join the demonstration.
"The head of state cannot just mediate and guarantee dialogue," Republicans Senator Pierre Frogier told a rally for the No vote in the referendum on Wednesday. "He is also the guarantor of French solidarity."