He did not provide specific details about the possible restrictions, but said the country would consider suspending some tourism permits.
The islands face a series of man-made problems including a growing population, illegal fishing of sharks and sea cucumbers, and internal disputes in the running of the national park.
The islands' official population is 18,000 but growing fishing and tourism industries are believed to have attracted around a further 15,000 people who live on the archipelago illegally according to government officials.
Martin Wikelski, a biologist at Princeton University, agreed that action needs to be taken to protect the Galapagos' ecosystem.
"The government needs to be stricter on what is allowed there as pressure on Galapagos grows," he said. "It is one of the world's most unique ecosystems... and continues to be one of the most important laboratories for evolution studies."
A United Nations delegation is also visiting the islands to determine whether the area, a world heritage site, should be declared "in danger."
The volcanic islands, located around 1,000km west of Ecuador, first came to prominence that inspired Charles Darwin's theory of evolution.
They are home to hundreds of unique species, including giant tortoises, exotic birds such as the blue-footed booby and iguanas.