He said his claim was incorrect and offended both Vietnam and Cambodia.
In a Facebook post on May 31 Lee had expressed condolences on the passing of former Thai PM and president of the Privy Council, General Prem Tinsulanonda, who he said served at the time five ASEAN members came together "to oppose Vietnam's invasion of Cambodia and the Cambodian government that replaced the Khmer Rouge."
Phuc expressed his unhappiness at talks he held with Lee on the sidelines of the 34th ASEAN Summit in Bangkok, Thailand, on Saturday.
He said history has proved that the statement on Vietnam’s position in the Khmer Rouge fight was inaccurate.
A prejudice like this negatively affects Vietnam and Cambodia, especially the families of hundreds of thousands of Vietnamese voluntary soldiers who sacrificed themselves to help the Cambodian people end the genocide by the Khmer Rouge to rebuild their country, he said.
The Ministry of Foreign Affairs said in a statement: "PM Lee Hsien Loong explained that Singapore did not mean to offend Vietnam. The purpose of recalling a hurtful chapter in Indochinese history was to remind people that peace and prosperity in ASEAN did not come from nowhere, and the countries in the association must maintain unity and solidarity and strengthen relations."
The two PMs said the talks helped both sides come to a better understanding and agreed to continue cooperating to strengthen and develop bilateral relations in all spheres.
Lee's post met with strong opposition, including from Cambodian PM Hun Sen who slammed it as an insult to the sacrifice of the Vietnamese military volunteers who helped liberate Cambodia from the genocidal regime.
The Khmer Rouge, led by Pol Pot, invaded Vietnam and killed tens of thousands of people between 1975 and 1979 as part of its genocidal agenda. At the request of Cambodian revolutionaries, Vietnamese soldiers marched into Phnom Penh in January 1979 during a counteroffensive on the southwestern border to free the capital from the Khmer Rouge's clutches.
This year’s ASEAN summit, with the theme "Advancing partnership for sustainability," is held on Saturday and Sunday, seeking to promote cooperation and strengthen the consensus process among ASEAN members to address new global challenges.