Japan last year pledged up to five billion dollars in aid over five years until 2013, provided the security situation allows projects to go ahead and contingent on guarantees the assistance will not be lost to graft.
It will be Karzai's fourth trip to Japan, and his first since he won his second presidential term last November in elections widely criticised as marred by ballot-stuffing and vote-rigging.
Talks with Japan's new Prime Minister Naoto Kan and Foreign Minister Katsuya Okada will focus on improvement of security and the wider development of the war-torn and dirt-poor central Asian nation.
"The quality of governance needs to be improved," Japanese Foreign Ministry press secretary Kazuo Kodama told AFP before the visit. "We do have sympathy for his challenges, but at the same time, in order for his government... to really succeed in addressing all these challenges, he has got to put his government in order," Kodama said. "So I think Prime Minister Kan and Foreign Minister Okada will certainly look forward to discussing these issues in a candid, straight-forward manner."
Japan, whose military is restricted by a post-World War II pacifist constitution, has not deployed troops to Afghanistan, but the world's second biggest economy is one of the biggest donors to the country.
Japanese aid has built 650 kilometres (400 miles) of highway and a new Kabul airport terminal, and its city planners are working to redevelop the capital, where more than 100 Japanese buses are now providing public transport.
Of the aid package pledged last year, about 980 million dollars have been disbursed, including more than 300 million dollars to pay the wages of Afghanistan's 80,000 police officers, Japanese officials say.
Other Japanese aid projects in the works are vocational training and small-scale rural aid projects that would help former Taliban foot-soldiers drop their arms and earn a living in civil society. However, massive graft threatens to undermine many international aid projects.
Watchdog Transparency International says Afghanistan has the worst corruption of any country except Somalia, which has no functional government.
Kodama said that Japan's foreign minister had repeatedly stressed that "this money comes from our taxpayers' pockets, and the government needs to be accountable for the way their money will have been spent. Money must be spent in an efficient and effective manner to meet the declared objectives."
Karzai's visit comes days after US officials said Afghanistan has mineral deposits worth at least one trillion dollars, including iron, copper, cobalt, gold and lithium.
Kodama said the US Defense Department report would likely be discussed, adding: "If Afghanistan is blessed with such abundant, precious mineral resources, we certainly wish that this asset is used for the people of Afghanistan to build the nation."
Karzai, after an audience with Emperor Akihito and meetings with Japan's leaders Thursday, on Friday plans to deliver a policy address at an event hosted by think-tank the Japanese Institute of International Affairs.
He is due to visit the Hiroshima Peace Memorial on Saturday to commemorate the victims of the US atomic bombing of the city at the end of World War II, then travel to the former imperial capital of Kyoto.
On Sunday he visits the nearby world heritage site of Nara -- another former capital that once marked the end of the Silk Road trade route which also ran through Afghanistan -- before leaving Japan later in the day.
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