Abe defended recent visits by his Cabinet members to the shrine in Tokyo, which honors Japan's war dead in World War II, include 14 designated as Class A criminals by the Allies during post-war trials.
The shrine has been a source of friction between Japan and its neighbors, South Korea and China. South Korea, where feelings are still strong against Japan's harsh colonial rule of the Korean Peninsula between 1910 and 1945, sees the shrine as symbolic of Japan's imperial past.
South Korea's protest follows its recent cancellation of the visit of its foreign minister to Tokyo over the visit of two Japanese ministers to the controversial shrine.
Japan's Kyodo News reported Thursday South Korea's Foreign Ministry summoned Japan's Ambassador Koro Bessho in Seoul to protest Abe's defense of the minister's visit to the shrine.
The report said Abe, while speaking in parliament about the reaction from South Korea and China, had said: "My ministers will not yield to any kind of intimidation."
South Korea's Yonhap News said First Vice Foreign Minister Kim Kyu-hyeon, in his meeting with Bessho, urged Japan to "correct its distorted understanding of history and anachronistic remarks."
"We sincerely hope Japan [will] squarely face its past and correct its wrong perception and remarks, while thinking of enormous the pains and damages caused by Japan's colonial rule and invasion," Kim was quoted as telling the Japanese envoy.
Yonhap said while ignoring concerns of South Korea and China, about 170 Japanese lawmakers also had visited the shrine this week.