Lee Myung-bak flew to the islands, which are known as Dokdo in South Korea and as Takeshima in Japan.
A Kyodo news agency report said Japan had summoned South Korea’s ambassador to protest against the visit.
Both South Korea and Japan say they have a historical claim to the islands, and the issue has been a long-standing thorn in relations.
The islands, which are roughly equidistant from the two countries, are small but lie in fishing grounds which could also contain large gas deposits.
South Korea has controlled them since 1954 and stations a small coastguard detachment on them.
Lee Myung-bak is the first South Korean leader to visit the islands. The visit was announced by his spokeswoman early on Friday.
“If the visit is made, it would go against our country’s position and so we strongly urge its cancellation,” Japanese Foreign Minister Koichiro Gemba told journalists.
“We must respond to it firmly.”
He said the visit “would definitely have a large impact” on ties.
The South Korean president was first due to visit Ulleung Island before flying on to the disputed area, his spokeswoman said.
Lee Myung-bak’s visit comes with the two countries’ football teams due to play off for the Olympic bronze medal later in the day.
It also comes shortly before South Korea marks the anniversary of the end of Japanese colonial rule.
Disputed islands:
• Known as Dokdo (Solitary islands) in Korea, Takeshima (Bamboo islands) in Japan
• Also known as Liancourt rocks
• Claimed by Japan and South Korea, but occupied by South Korea since 1954
• Just 230,000 sq m in size, with no fresh water
• Surrounding waters valuable for their fishing
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