A cross-party group of parliamentarians said 110 members paid homage at Yasukuni Shrine in downtown Tokyo, a spot condemned by China and Korea as a symbol of Japan's militarist past.
The visit came just hours after Abe shook hands with Chinese Premier Li Keqiang on the sidelines of an Asia-Europe summit in the Italian city of Milan, despite tensions between the two powers.
Earlier media reports said the brief exchange of pleasantries -- the first time the two men have met -- took place after news of the shrine visit broke, but a Japanese foreign ministry official later clarified that they shook hands late on Thursday evening.
The handshake came as the latest sign of a thaw, with Japan pressing for a summit with Chinese President Xi Jinping next month. But the shrine offering in Abe's name sparked fresh anger in Beijing once again.
More From This Section
The offering was made as a cross-party group of 110 Japanese parliamentarians paid homage at the shrine to mark the start of a four-day autumn festival.
Abe, who sent a potted tree with his name and title prominently displayed, is thought unlikely to go even after he returns home tomorrow from the summit in Italy.
China reacted with renewed anger today.
"China is gravely concerned and firmly opposes the negative activities in Japan surrounding the Yasukuni Shrine," foreign ministry spokesman Hong Lei said in a statement.
"China would like to reiterate that Sino-Japan relations can only realise healthy and stable development when Japan seriously faces up to and repents of its aggressive past and disassociates itself with militarism," he added.
Taiwan, a Japanese colony until 1945, also offered a rebuke, saying visits hurt "people's feelings in neighbouring countries".
The 145-year-old Shinto shrine is the supposed repository of the souls of some 2.5 million citizens and soldiers who died in World War II and other conflicts.
They include senior figures in the WWII administration, such as General Hideki Tojo, who ordered the attack on Pearl Harbor.
Japanese nationalist politicians who go to the shrine claim there is nothing wrong with honouring war dead.