The military is reported to have taken away the bodies of those killed, and the true number of deaths may never be accurately established.
Witnesses told local media that soldiers had used heavy weapons and had shot at anything that moved.
More than 600 people have been killed since last month's military coup.
The military has resorted to increasing levels of violence to maintain its grip on power.
The latest killings in Bago, near the main city of Yangon, are reported to have happened on Friday but took a whole day to emerge as many residents were forced to flee to nearby villages.
Monitoring group the Assistance Association for Political Prisoners (AAPP) said the actual number of deaths was likely to be much higher.
The Myanmar Now news outlet quoted protest organiser Ye Htut as saying: "It is like genocide. They are shooting at every shadow."