Yasushi Akashi, whose country is a major donor to Sri Lanka, ended a five-day visit saying he detected a "lack of flexibility and openness" in the government's attempts to promote reconciliation on the island.
His remarks followed an announcement by the UN that a panel would be named this week to advise Secretary General Ban Ki-moon on accountability in Sri Lanka.
The panel is seen as a precursor to a full war crimes probe into the last months of the conflict, when government troops finally defeated the Tamil Tiger separatist rebels in May 2009 after decades of bloodshed.
The UN has said that at least 7,000 civilians were killed in the first four months of fighting last year.
The war ended when the military killed the leadership of the Liberation Tigers of Tamil Eelam (LTTE), which had been fighting for independence since 1972.
Akashi said he had pressed Colombo to allow the UN to get involved in Sri Lanka's reconciliation process.
"The government listened to what I said. (