Shinzo Abe said his visit to Yasukuni was an anti-war gesture.
But China called the visit “absolutely unacceptable to the Chinese people”, and Seoul expressed “regret and anger”.
China and South Korea see Yasukuni as a symbol of Tokyo’s aggression during World War Two, when Japan occupied large parts of China and the Korean peninsula.
The US embassy in Tokyo said in a statement it was “disappointed” and that Shinzo Abe’s actions would “exacerbate tensions” with Japan’s neighbors.
China, Japan and South Korea are embroiled in a number of disputes over territory in the East China Sea.
It was the first visit to Yasukuni by a serving prime minister since Junichiro Koizumi went in 2006.
Shinzo Abe, who took office in 2012, entered the shrine on Thursday morning, wearing a morning suit and grey tie. His arrival was televised live.
“I chose this day to report [to the souls of the dead] what we have done in the year since the administration launched and to pledge and determine that never again will people suffer in war,” he said.
“It is not my intention at all to hurt the feelings of the Chinese and Korean people.”
Officials said Shinzo Abe visited Yasukuni shrine in a private capacity and was not representing the government.
But Chinese Foreign Ministry spokesman Qin Gang said: “We strongly protest and seriously condemn the Japanese leader’s acts.
“This poses a major political obstacle in the improvement of bilateral relations. Japan must take responsibility for all the consequences that this creates.”
Japan made an unwritten agreement with China in the 1970s that serving leaders would not visit the shrine.
But now, Shinzo Abe appears to have broken that deal.
In August, Shinzo Abe sent a ritual offering to the shrine but was not among a group of dozens of Japanese politicians who visited Yasukuni.
During an earlier period in office between 2006 and 2007 he said he would not even discuss visiting the shrine “as long as the issue remains a diplomatic problem”.
Yasukuni commemorates some 2.5 million Japanese men, women and children who have died in wars.
But the souls of hundreds of convicted WW2 criminals are also enshrined there.
Fourteen so-called Class A criminals – those who were involved in planning the war – are among those honored. They include war-time leader General Hideki Tojo, who was executed for war crimes in 1948.
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