Macron issued an order calling for the 221 hectare site to be cleared as he was concerned that the site could become a magnet for ecologists and anarchists.
Interior minister Gerard Collomb: said: “We don’t want places where there is no law and order in France.”
The protesters are concerned the area will suffer from nuclear pollution for hundreds of years to come.
Three of the protesters, who call themselves “owls”, were arrested during the police swoop and another demonstrator was arrested for attempting to throw an incendiary device at police.
One protester told AFP: “We are here because we don’t want the Earth to be poisoned.
“We are on this old oak tree which has lived far longer than us”.
Benoit Hamon, the socialist candidate in last year’s elections, said: “I think it would be better to engage in dialogue and take a real interest in what the residents of this area think”.
The protesters have stopped any planned exploratory drilling work from taking place so far.
President Macron is keen to crack down on protester-occupation movements after one last years at a site earmarked for a new developed near Nantes.
The protesters started camping in the Bois-Lejuc in June 2016, when Andra, the French national radioactive waste management agency, started clearing the territory and erecting a wall around it.
Mr Collomb wrote on Twitter: “Under the authority of the prefect of the Meuse, an operation led by the national gendarmerie began this morning at 6:15am to end the illegal occupation of BoisLejuc.”
The occupation of the protesters took place at the site where ventilation chimneys are to be installed.