Seoul city mayor Park Won-Soon said the zoo would temporarily suspend its daily show, which is performed by three Indo-Pacific bottlenose dolphins, from next Monday.
Animal rights activists have called for the release of the dolphins, saying one called "Jedol" was illegally captured last July by fishermen off the southern resort island of Jeju.
"I believe Jedol must be allowed to swim freely," Park told reporters.
Park, a longtime liberal activist, won the mayoralty last October in a shock upset for the ruling conservative party. He joined the main opposition party last month.
The zoo said the 13-year-old Jedol would be reintroduced into the wild in March 2014 after gradual adjustment training.
It said the other two dolphins would be kept in captivity because they were old and weak.
Zoo officials said they would decide whether to permanently cancel the show after gathering opinions from experts, activists and citizens.
South Korea's law bans the unauthorized seizure of dolphins and whales.