It said the "damning" information on the new driver-only-operated (DOO) services came from passengers and rail workers.
Southern said industrial action and a drivers' overtime ban had displaced its on-board supervisors "on occasions".
A 24-hour walkout by RMT conductors on the Southern network over changes to their roles is under way.
Southern is replacing conductors with on-board supervisors (OBS) who would no longer be in charge of closing train doors.
The company has said the changes it is making are "small" and "safe".
But the RMT believes public safety is at risk.  It also says a second member of staff on trains is critical.
The union said that, in previous correspondence to MPs, Southern anticipated 0.06% of trains would run without an OBS, the equivalent to one service, every two days.
But the RMT said information provided for five days - 9, 12, 14, 15 and 18 January - suggested 15 trains travelled without one. It said this was at least six times more trains than promised.
RMT General Secretary Mick Cash said the union believed the instances of trains running without a second person were "far more widespread and will rapidly and substantially increase".
A Southern spokesperson said: "Last-minute changes to some services caused by the industrial action and the drivers' overtime ban has displaced the on-board supervisor so that, on occasions, they've not been able to join the train.
"Previously, this train would have had to be cancelled but we can now run the service and avoid disrupting hundreds of passengers."
Many more Southern trains than promised are travelling without a second member of staff, the RMT union has claimed.