In a study published in the journal Aquatic Conservation, Rodolphe Devillers says protection is often granted in areas where it won't inconvenience fishing and other industrial activities — a method he says is at odds with preserving wildlife.
Meanwhile, regions that house at-risk species as well as fishing or industrial operations are frequently neglected because governments fear the economic and political costs of interfering with business, he says.
"Are you going to give a bodyguard to somebody that's at no risk, to somebody living alone in his village, or are you going to give a bodyguard to somebody who may face an attack?" he said.
"If there's nothing to protect from, what's the point?"
After analyzing a global database of more than 5,000 protected marine areas, Devillers and his team found that about 10 account for more than half of all protected waters.
Nine of those 10 included areas that were not under threat, he said.
If countries are serious about conserving wildlife, they must be willing to make economic sacrifices, he said.
"We cannot think that by having no impact on our life, we are going to protect our planet," he said.
He said that in Canada, for example, scientists' top picks for protection are often ignored in favour of regions that have little industrial activity.
The Department of Fisheries and Oceans didn't make its scientists available for comment over the weekend.
However, a spokesman for the department said Ottawa has taken steps to protect the country's oceans.
"Over the past five years, Fisheries and Oceans Canada has added new marine protected areas and identified several more areas of interest, a key step in the establishment of a marine protected area," spokesman Frank Stanek said in an email.
One per cent of Canada's waters are designated as protected areas, the department said.
The United Nations Convention on Biological Diversity has a target of protecting 10 per cent of coastal and marine areas worldwide by 2020.