THE HAGUE — For two years, Pascal Husting’s employer paid to fly him most weeks between his home in Luxembourg and his office in Amsterdam.

Such trips are common for executives at major international corporations in Western Europe.

But Mr. Husting isn’t working for a corporation. He is the international program director for Greenpeace, the nonprofit that is arguably the world’s most high-profile environmental advocacy organization.

Mr. Husting’s weekly commute prompted a chorus of derision from Greenpeace opponents after “Flygate” was revealed in Dutch media this summer.

It also aroused the anger of activists, staff members and donors who have long supported the 40-year-old group. Traveling 500 miles round trip in a carbon-emitting airliner was hard to square with Greenpeace’s aims, after all.

“Arrogance is a word that springs to mind,” Greenpeace donor Altwin de Moor wrote on his personal blog. “It seems as if those at the top of Greenpeace are more interested in watching each other’s backs than standing up for the right thing. I will be keeping an eye on developments and decide on the basis of what happens whether to cancel my donations.”

The revelations followed another damaging acknowledgment by Greenpeace: A blunder by its finance department resulted in $5 million in losses on foreign exchange markets — a rare peek into the internal workings of an advocacy group associated with saving whales and protecting trees.

Many wonder what’s next for Greenpeace, which has headquarters in Amsterdam and operates on a $95 million annual budget that supports 28 branch offices, 2,400 employees and 15,000 volunteers around the world.

Arco Timmermans, a professor of public affairs at Leiden University, said the scandals show how Greenpeace “has become a victim of its own success” and that the group is having trouble balancing its activism with its operational needs.

Unlike most other major enterprises, Greenpeace has to give a nod to the environment in conducting its business.

Each of Mr. Husting’s round-trip flights generated 313 pounds of carbon dioxide. He flew between Luxembourg and Amsterdam as often as once a week — normal for a banker but too much for many of Greenpeace’s environmentalists. The total cost of his flights over two years was around $20,000.

Mr. Husting issued a public apology on Greenpeace’s website saying he “ignored the voice of my own conscience.”

He pledged to start making a 12-hour round trip by train, but the damage is done.

In the Netherlands alone, nearly 700 donors have canceled contributions to Greenpeace in response to the news of Mr. Husting’s flights.

As the public relations disaster became clear, more than 40 Greenpeace staff members signed a letter in July demanding Mr. Husting’s resignation and asking Greenpeace Executive Director Kumi Naidoo to “reflect” on his own job.

Mr. Husting was unable to relocate his family to Amsterdam, so Mr. Naidoo exempted him from an in-house rule to take overland routes for trips of less than 320 miles.

The special treatment didn’t sit well with rank-and-file workers. Many employees felt that Mr. Naidoo’s logic was similar to corporations that talk about curbing greenhouse gases but shirk from inconveniencing their executives.

“Externally, this flying scandal seriously undermines our credibility as an organization,” the employees wrote in the July letter, which was printed in Dutch media. “Every time we criticize politicians or companies, this story will come back [to haunt us]. If Greenpeace does not walk the talk, why should others do so? You do not seem to understand how public opinion works.”

Some say Flygate is only the beginning.

Mr. Naidoo has told local media that staffers sometimes are put under “unfair pressure” to sign off on unauthorized expenses.

Dutch journalists also revealed that the head of Greenpeace’s Dutch office, Sylvia Borren, had flown to Bangladesh, New Zealand, Peru and South Africa in the same year for business and personal reasons. Ms. Borren, who has family in New Zealand, issued a statement saying the flights were “of vital importance for my work and [only] in part for my private life.”

Greenpeace has since hired a new finance director and commissioned external audits to prevent further scandals.

Mr. Timmermans, the public affairs professor, said these measures are insufficient and the advocacy group needs to do more.

“No organization can change without making hard decisions,” he said. “Friction is not a bad thing, but the question here is whether this is friction you can control. If Greenpeace changes its management culture, it will improve its survival chances in the long run, but it’s going to be painful.”

The employees’ letter demonstrates how they used the same aggressive campaigning tactics usually reserved for polluters against their own leadership, he said.

“I think this has been going on internally not just for a few months, but longer,” Mr. Timmermans said.

Greenpeace spokesman Andrew Kerr said the organization’s international board ultimately would decide whether Mr. Naidoo handled the situation properly.

“It was an error of judgment which everybody regrets and Pascal has apologized for,” the spokesman said. “Kumi has not asked for Husting’s resignation. Ultimately, that’s the decision he has to make as executive director.”

But, Mr. Timmermans said, “I don’t think there is a way back.”

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