The exercise was carried out in the Darwin Wolf marine reserve by experts from Ecuador, Japan, Spain, Britain and New Zealand, biologist Harry Reyes told EFE.
Researchers had to operate at depths as low as 37m to perform ultrasound on four whale sharks - three females and a male.
The team also took blood samples from two of the sharks.
The whale shark, the world's largest fish, can extend more than 15m in length, Reyes said.
Tests found no evidence that any of the females was pregnant, according to Reyes, the director for conservation of marine ecosystems at Galapagos National Park.
He said scientists need to learn more about the whale shark to better design measures aimed at protecting the species.
The team included experts from the Churashima Foundation on the Japanese island of Okinawa, where several whale sharks are kept in captivity.
