In an interview with The Associated Press on the sidelines of the U.N. General Assembly, Foreign Minister Kim Sung-hwan said: "We are victims of Japanese colonial rule."
Kim, speaking a few hours before "serious" talks with Japan's foreign minister, also said South Korea would not compromise in its dispute over the tiny Dokdo islands, called Takeshima by Japan, which has further strained ties.
"When the Japanese government claims Dokdo is their territory, Korean people (take) it as another attempt to invade our country," Kim said. "So that's the Korean sentiment and I hope that the Japanese government understands this."
But he said South Korea recognizes its shared interests with fellow-democracy Japan, such as coping with North Korea and its nuclear ambitions. Both Japan and South Korea play host to tens of thousands of U.S. troops.
Kim said Seoul wants to expand relations with Japan, including in military cooperation, but only if South Korean public sentiment allows it. In June, they put on hold an intelligence sharing pact after it provoked an outcry in South Korea.
"We have to try to overcome these differences. It's up to the Japanese attitude. While they maintain their attitude ... there should be some limit on the scope of cooperation," he said.
Japan occupied the Korean peninsula for 35 years until the defeat of fascist forces in World War II and also occupied much of China. Japan issued a formal apology in 1993 over its use of Korean women as sex slaves by its soldiers during the war, but has failed to convince South Korea it is truly contrite.
Kim accused Japanese politicians of denying war crimes and said Japan's failure to educate its people properly about the past was the root cause of its various territorial disputes over islands in the region— including with Russia and Asia's premier power, China.
"It's in sharp contrast with what Germany did to get the support and respect from the neighboring countries" after World War II, Kim said. "If Japan does it, I'm sure they can (get) respect from neighboring countries."
The dispute escalated last month when South Korean President Lee Myung-bak made an unprecedented visit to Dokdo, which drew unusually stern criticism from Japan. South Korea has rejected a Japanese proposal for the dispute to be settled in the International Court of Justice.
On Wednesday, Japanese Prime Minister Yoshihiko Noda stuck by Japan's stance on the islands, but said it did not want it to adversely affect relations with South Korea.
The issue stirs particularly strong nationalist passions among Koreans, as Japan's takeover of Dokdo in 1905 presaged its annexation of Korea five years later. South Korea took the islands back in the early 1950s and deploys police there.
Kim and Japan's Foreign Minister Koichiro Gemba discussed the island dispute and historical issues including "comfort women," in their 30-minute meeting Thursday, said Japanese ministry spokeswoman Naoko Saiki. She would not disclose the substance of the exchanges but characterized them as "serious."
Saiki said they also discussed North Korea, and that despite the current difficulties between Japan and South Korea, the ministers agreed they have to cooperate and strive for "stable, forward-looking relations."
In the interview, Kim said that South Korea remains open to better relations with North Korea, and that it was disappointed when its offer earlier this month to provide flood relief to North Korea was rebuffed as inadequate by Pyongyang.
He also said that since North Korea's failed attempt in April to launch a satellite, "Trust has regressed." The unsuccessful launch was deemed by the U.S. to have military implications and to violate prior agreement by North Korea to suspend ballistic missile testing.
In spite of North Korea's new leader, Kim Jong Un, setting a somewhat more modern and open style, there has been no practical improvement in relations with South Korea or the United States with Pyongyang.
The United States, China and South Korea are all going through elections or leadership changes late this year, Kim noted, suggesting that any significant resumption of diplomatic activity with North Korea may have to wait.