Wardens have been occupying park offices since Cepeda's appointment was announced
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Ecuador officials say police have taken control of the Galapagos Islands national park following a row over the appointment of a new park director.
Park wardens protesting against the appointment have been involved in clashes with local fishermen.
The wardens say the president is treating the directorship as a political favour, and the constant changes are hampering their work.
The new park director, Fausto Cepeda, is the eighth in two years.
Mr Cepeda has now been installed in his office, but only after violent confrontations between the park wardens occupying the buildings, and groups of fishermen throwing stones and wielding saws and cutlasses.
"I'm in my office. I'm in control. And I'm trying to lower the tension," the Associated Press news agency quoted him as saying.
The BBC's Elizabeth Blunt says the fishermen are backing Mr Cepeda in the hope that he will relax the tight restrictions on fishing for lobsters and sea cucumbers enforced by his predecessor, biologist Edwin Naula.
Environmentalists' praise
The fishermen themselves went on strike earlier this year, and blocked all entrances to the national park for a time to press their demands.
The giant tortoise is one of the unique attractions of the islands
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Mr Naula was praised by environmentalists for his efforts to protect the islands' fragile ecosystem.
Announcement of his replacement prompted around 300 wardens to occupy research stations on the islands.
The Galapagos are marketed by tour companies as The Enchanted Islands, a beautiful and peaceful holiday destination of unique natural and scientific interest.
This was where the scientist Charles Darwin first noticed that creatures isolated on different islands had developed differently, and went on to develop his theory of evolution.
The Galapagos are still home to populations of sea lions and giant tortoises which draw thousands of visitors a year.
But our correspondents says that over the years more and more people have settled in the previously uninhabited islands, including growing numbers of fishermen, who naturalists say are now threatening their unique environment.