The 9,000-page collection of files was assembled by a Pentagon task force in the early 1970s - which the Los Angeles Times said proved that atrocities by US forces had gone far beyond what public records had shown.
The crimes committed also went largely unpunished, the newspaper said on Sunday.
The Times report is based on records of the Vietnam War Crimes Working Group at the National Archives in College Park, Maryland.
Among the events substantiated by the records were seven massacres in Vietnam from 1967 to 1971 in which at least 137 civilians died
The files do not include the notorious 1968 massacre of about 500 civilians at My Lai village.
There were 78 other attacks on non-combatants in which at least 57 people were killed, 56 wounded and 15 sexually assaulted.
In total, 320 incidents of abuse by US soldiers are substantiated, the paper said.
"Abuses were not confined to a few rogue units," the Times reported.
"They were uncovered in every army division that operated in Vietnam."
The Vietnam report comes as the military investigates alleged abuse of Iraqi civilians by US soldiers, including the killing of 24 people in Haditha and a quadruple murder and rape in Mahumdiya.
A quarter of the 203 soldiers accused of harming Vietnamese civilians or prisoners were court-martialled, but only 23 were convicted, according to the newspaper's review.
The documents were first released in 1994 - 20 years after the group closed its probe - and moved to the archive.
The collection includes 241 case summaries that chronicle more than 300 substantiated atrocities by US forces and 500 unconfirmed allegations, according to the Times.
The newspaper said it examined most of the files and obtained copies of 3,000 pages, or one third of the total, before government officials removed them.