Earlier this month, South Korea notified the International Whaling Commission (IWC) that it planned to lift an all-out whaling ban and start catching the animal for scientific purposes only in immediate waters surrounding the Korean Peninsula, reportsYonhapNewsAgency.
But the plan prompted an international outcry, with some countries urging Seoul to reconsider.
"Discussions between government ministries have been concluded in a way that effectively scraps the plan to allow whaling in coastal waters," a senior official said on condition of anonymity.
"Even if it is for scientific research, we have to take into consideration that this has emerged as a sensitive issue at home and abroad."
Officials from the presidential office, the Prime Minister's Office and the agriculture and fisheries ministry held a meeting recently to discuss the issue, sources said. President Lee Myung-bak also reproached Agriculture Minister Suh Kyu-yong as international criticism grew, they said.
South Korea has recently suggested it may scrap the whaling resumption plan, with ministry officials saying the country may choose not to resume whaling should there be other means to study marine mammals in South Korean waters.
South Korea has banned catching any type of whale since 1986 even though the IWC charter bans whaling of only 12 specific species of whale.
The government said one of the reasons for resuming scientific whaling was to limit the number of whales in its home waters, estimated at about 80,000.
The whales in South Korea's adjoining waters are believed to be eating some 146,000 tons of fish annually, about 12 percent of the country's annual fisheries production, according to the ministry.
Whale meat remains popular in the coastal towns of South Korea with whales accidentally caught in nets remaining the only source of such meat.