The Australian striker has yet to feature for the Teessiders this season despite being their highest-paid player and Mowbray's recent comments have probably done nothing to instil confidence in the former Celtic star.
"There is no Scott McDonald situation," he said.
"Will we see him back in the team? I don't know.
"Scott McDonald has to keep doing what he does in training, keep working hard and try to get himself into the team."
He added: "I have to say, with total respect to Scott McDonald, that he's been here two years and he hasn't scored a bagful of goals.
"But it's a question I understand people asking because he cost a lot of money.
"But with respect to Scott McDonald, he's just another name on my team sheet or not on my team sheet.
"Scott just needs to get his head down and keep working hard and see what happens."
McDonald was linked with a Riverside Stadium departure during the summer and could still be sent out on loan according to reports.