They would like better physical protection for the sites and believe they should be showcased.
"You've got an impressive body of rock art here," said Dr Clottes, who has written more than 300 scientific papers and led studies into France's Chauvet Cave, chronicled in a documentary by director Werner Herzog.
"They are the product of Maori culture and their beliefs. They didn't just do these in idle time, it was very, very meaningful for them - I would say probably powerful."
Dr Clottes said much work would have gone into the rock art at Kaingaroa, with some of its 40 rock carvings of waka stretching 3m long.
Who created them is unclear, but it's believed the carvers may have been of the people of Te Marangaranga, who had been defeated by other tribes and driven from the area.
The site, held to be the North Island's most spectacular example, was rediscovered in 1925 by forestry explorers and soon after described as a national monument by anthropologist Sir Peter Buck.
Over decades, it had been obscured by mosses, lichens and ferns, and some of its carvings defaced by vandals.
Local iwi Ngati Manawa recently took over the land and, as kaitiaki or guardians, wish to protect it for future generations.
"They have to be protected, studied in depth and made known to the public," Dr Clottes said.
"This is part of your cultural heritage and people should know about it."
Auckland couple Peter and Pam Russell have inspected many sites - among them art in hard-to-reach sea caves in Taranaki and Coromandel - and have also pressed the Government on the issue.
Mr Russell said there had been little research on the sites and doubted the cost involved in protecting them would be small.
Historic Places Trust restorer Jim Schuster said that at last count there were 550 rock art sites in the South Island and 107 in the North Island.
Given their remote locations - many were hidden on farmland - Mr Schuster expected hundreds more were waiting to be rediscovered in the country's wilderness.
"They're under-appreciated," he said.
"When people talk about Maori art, they talk about carvings - the things you see that are out there in your face, for tourists - but with rock art, you've got to go a long way into the bush to see it.
"And they are rare - when you look at the number of meeting houses and the number of rock art sites, there's a big difference."