Hirohito visited the Yasukuni Shrine eight times after the war to pay his respects for those Japanese who died in 11 wars.
But, according to a former palace official's journal from 1988 published in the Nihon Keizai Shimbun newspaper on Thursday, he halted his visits in 1978, saying "At some point, Class-A criminals became enshrined.
"That's why I have not visited the shrine since. This is my heart."
It is believed the Shinto shrine's head priest secretly enshrined 14 top, or Class-A, war criminals in 1978.
The revelation has led to criticism of Japanese prime minister Junichiro Koizumi’s ongoing visits there. He is due to visit it again next month.
Japan's ties with China and South Korea have chilled since Koizumi took office in 2001 and began his visits to the shrine, where World War Two leaders convicted as war criminals by an Allied tribunal are honoured along with the nation's 2.5 million dead.
The shrine is seen by critics at home and abroad as a symbol of Japan's past militarism.
An imperial household agency spokesman declined to comment on the report, saying it was about a private memo.
Hirohito's son and heir, Emperor Akihito, has not visited the shrine since ascending the throne in 1989 but the country's prime minister, Junichiro Koizumi has been each year since he took office.
Koizumi, who steps down in September, said the Hirohito revelations would not change his stance.
Koizumi says visiting the shrine
is up to the individual
"Different people have different feelings. So it is not a matter that I shall dictate on. One is free to visit or not to visit," Koizumi told reporters.
He held firm against the proposal of removing the names of the war criminals, which constitutes a sacrilege to Shinto priests.
The shrine has now become an issue in the race to succeed Koizumi.
The chief cabinet secretary and frontrunner in the race, Shinzo Abe, has backed Koizumi's visits but has not said whether he would make similar pilgrimages if elected.
Potential rival Yasuo Fukuda has said he favours a new memorial for the war dead.
The Yasukuni shrine was built in 1869 by the Emperor Meiji and became a symbol of state Shintoism under which the sovereign was revered as a god in whose name war was waged.
It was supported by the state until the end of 1945.
A US-led tribunal hanged seven of the 14 Class-A war criminals enshrined at Yasukuni. US occupation authorities did not prosecute Hirohito, who renounced his divinity and continued his reign.
Shrine authorities have never accepted the results of the Allied war tribunal as valid and consider the wartime leaders honoured there to be "Showa martyrs".
Former Imperial Household Agency Grand Steward Tomohiko Tomita, who died in 2003, reportedly left more than 20 notebooks recording his conversations with the late emperor.
Some academics say the late Hirohito's own responsibility for the war has never been fully pursued in Japan, largely due to the decision by US occupation authorities to keep him on the throne and turn the emperor into a symbol of a newly-democratic Japan.