The Goro Nickel mining company in New Caledonia says Unesco made the reef a world heritage site with the full knowledge of there being an industry in the area.
The 15,000 square kilometre reef area includes a lagoon in the south, where activists have campaigned against a Goro Nickel company waste pipe, saying it will contaminate the area.
The deputy managing director of Goro Nickel, Jean-Francois David, says the plant won't pose any problem.
"Unesco has decided to inscribe all the zones, including the south zone which is in contact with Goro Nickel. So it means there is absolutely no conflict between what we are doing and the interest of the lagoon."