The sites, in south Vietnam, are areas where specific incidents are believed to have taken place. Officials declined to elaborate, citing concerns for the families of the missing.
The Defence Department's POW/Missing Personnel Office says 1275 Americans are still unaccounted for from the Vietnam war. The office has so far investigated 600 cases.
Contact between the two countries has increased in recent years amid concerns among Washington and Asian allies about China's growing assertiveness in the region.