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."

He worked closely with owner Randy Lerner, who put the club up for sale last May but is yet to find a buyer.
The resignation of American Fox after 18 months at the Premier League's bottom club follows the departure of sporting director Hendrik Almstadt and three new appointments to the board.
Fox said "it makes sense for me to seek another challenge" following the changes in the Villa boardroom.
Villa are nine points from safety at the foot of the league and Fox and Lerner have been the target of fans' anger over their struggles.
Steven Hollis became the club's new chairman in January while former Governor of the Bank of England Lord King and ex-Football Association chairman David Bernstein have become directors at Villa Park.
And Gulf War commander General Charles Krulak is now listed as a director on the Companies House website.
In a statement Fox said: "The owner made it very clear last summer that he and I would seek to recruit a board that would put the club in a stronger position in the event that a sale didn't happen.
"As the board has taken shape, however, it has become clear that my role also has changed. While I am supportive of where the board is trying to take the club, it is my feeling that given the changes they are making, it makes sense for me to seek another challenge."
Many more Southern trains than promised are travelling without a second member of staff, the RMT union has claimed.
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Aston Villa chief executive Tom Fox has stepped down with immediate effect.