Hun Sen was a junior member of the Khmer Rouge but fled to Vietnam when the group split. He returned with the Vietnamese army that intervened in late 1978 to oust Pol Pot's Khmer Rouge and rose to power in a government set up by Vietnam.
Hun Sen said Lee's comments were an "insult to the sacrifice of the Vietnamese military volunteers who helped to liberate Cambodia".
Lee made similar comments at a security forum in Singapore on the weekend, noting how Vietnam's invasion of Cambodia had posed a serious threat to non-communist countries in the region.
On Tuesday, Vietnam's foreign ministry said it had raised the issue of Lee's comments with Singapore.
"Vietnam finds it regrettable that certain elements of the speech did not view history under an objective lens, causing negative impact on the public opinion," spokeswoman Le Thi Thu Hang said in a statement.
The Singaporean Embassy in Phnom Penh did not respond to a request for comment. A spokeswoman for Lee had no immediate comment.
Through the 1980s, Singapore along with other ASEAN and Western countries recognised a three-faction "coalition government" in exile, which included the Khmer Rouge. The factions battled Vietnamese forces in Cambodia from sanctuaries on the Thai border.
Vietnam withdrew its forces from Cambodia in late 1989, paving the way for a 1991 treaty that officially ended the war. Vietnam joined ASEAN in 1995 and Cambodia joined in 1999.
