Yasushi Akashi's visit to the lagoon district of Batticaloa came on the same day that two murdered Red Cross workers from the minority ethnic Tamil community were buried in the area, officials said.
"He is meeting several officials involved with resettlement of internally displaced people to get a first hand idea of the process," said a government official in Batticaloa, 300 kilometers (185 miles) east of Colombo.
An opposition lawmaker told parliament here Thursday that a senior police officer and a former air force officer were involved in last week's killing. The government did not immediately respond to the allegation.
Akashi held closed-door talks with Rajapakse at the president's tightly-guarded Temple Trees residence late Wednesday, and later met with representatives of the main opposition.
The Japanese diplomat arrived in Sri Lanka on Tuesday, shortly after heavy weekend fighting between government troops and the Tamil Tiger rebels in the island's north left scores dead on both