The incident occurred this morning on the BBC News Channel when Schafernaker gave a one-finger salute to Simon McCoy after he made a lighthearted remark.
After realising that the camera was on him, Schafernaker quickly tried to hide the gesture by moving his hand up to rub his face, but the damage had already been done.
McCoy immediately tried to amend for the incident by saying: "Every now and then there's always one mistake, that was it."
In a statement, a BBC spokesman apologised for the incident and confirmed that the corporation had received seven complaints about the gesture.
"Tomasz was not aware that he was on air, and whilst the gesture was only shown for a second, it was not acceptable," he said.
"The News Channel presenter live in the studio acknowledged a mistake had been made, and we apologise for any offence caused."