They met with Rafael Grossi in a tense meeting in Seoul that took place while protesters screamed outside the door.
Grossi, the International Atomic Energy Agency's director general, arrived in South Korea over the weekend to engage with government officials and critics and help reduce public concerns about food safety.
The IAEA last week approved the Japanese discharge plans, saying the process would meet international safety standards and pose negligible environmental and health impacts. South Korea's government has also endorsed the safety of the Japanese plans.