The regulatory Korea Communications Commission will send a letter of complaint to Pyongyang while other agencies will address the issue at international organisations, the transport ministry said in a statement.
The South says the North began the jamming in late April, affecting the GPS signals of aircraft using Seoul’s Incheon and Gimpo airports or flying over the central area of the Korean peninsula.
Shipping has also been affected. Seoul officials say air and sea traffic can use other navigational equipment and safety has not been compromised.
The North has not commented on the accusation.
“We will urge the North to immediately stop sending jamming signals and refrain from a recurrence,” the ministry said, adding the signals were still coming from the North.
Seoul will complain to the International Telecommunication Union (ITU) and International Civil Aviation Organization (ICAO), it said.
“The act of jamming GPS signals… is against the ITU’s constitution and poses a threat to the safety of international aviation operations guaranteed by ICAO rules,” the ministry said.