"When I heard the news, I was so saddened, I could not even cry," she said.
Japan has always refused North Korea's demand for reparations for its colonial rule and wartime oppression, saying Japan and Korea were not in a state of war.
The joint statement said Japan and North Korea had agreed on talks on economic aid and that details would be discussed during normalization talks.
Analysts say North Korea, hit hard by several years of natural disasters and chronic food and energy shortages, needs to improve ties with the West to secure desperately needed aid.
Tokyo gave South Korea US$500 million when they normalized ties in 1965. Analysts have said Tokyo could provide up to US$10 billion to the economically crippled North.
South Korean President Kim Dae-jung had been hoping Koizumi's trip would support his efforts to keep North-South ties on track.
Japan said it would send a senior official to Seoul today to brief the South Korean leader on the summit.
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