The leaders said nuclear experts would also share more data in future.
Japan was hit by an earthquake and tsunami on 11 March, which wrecked the Fukushima Daiichi nuclear plant.
Workers at Fukushima are still battling to control the stricken facility, which is leaking radioactive material.
China and South Korea have been critical of Japan's handling of the crisis in recent weeks.
But the BBC's Roland Buerk in Tokyo says the meeting was designed to show solidarity after the earthquake and tsunami. the three leaders promised they would work more closely on nuclear issues.
"We decided to strengthen co-operation in information sharing. In addition, we also decided to start discussion on establishing early notification framework in case of emergency and exchanging experts," the statement said.
South Korea and China had previously expressed concern that the nuclear leak was having an impact on food safety across the region.
But Mr Kan has been keen to highlight that food from his country is not contaminated.
During a photo opportunity on Saturday, Mr Wen and Mr Lee both ate food in the Fukushima prefecture.
Mr Wen and Mr Lee are the first foreign leaders to visit Fukushima - about 220km (136 miles) north-east of Tokyo - since the disaster.
Mr Lee said South Korea would do all it could to help reconstruction work in Japan.
The leaders of the three countries have met on an informal basis for a decade. Since 2008, they have held an annual meeting.
The massive earthquake tsunami left more than 24,000 people dead or missing.