Reports emerged on Thursday suggesting Rovers owners Venky's were conducting an inquiry into the terms of former manager Henning Berg's contract.
Shaw, it was claimed, had been told to steer clear of Ewood Park while investigations remained ongoing.
But a statement on the club website read: "Blackburn Rovers have acted to quash rumours regarding the position of managing director Derek Shaw.
"The club's owners wish it to be known that, contrary to those widespread rumours, Mr Shaw is very much with the club and insist that all other recent reports are untrue."
Former Preston chairman Shaw was appointed to his Blackburn role in June.
Rovers have had five managers - either in a permanent or caretaker capacity - since then, and Berg's spell in charge lasted just 57 days.