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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.”