Owen returned to action for Newcastle at the weekend just eight days after a double bout of surgery and is now set to play for England against Estonia and Russia in the vital double header.
McClaren rejected suggestions he and Newcastle boss Sam Allardyce were at loggerheads over whether Owen played and insisted the striker would feature so long as he was fit.
"People talk of a conflict between Newcastle, Michael and ourselves and there is nothing further from the truth," he said.
"We liaise with the club, the medical people, we liaise with (manager) Sam (Allardyce), we liaise with the player. No risk will be taken but Michael is a very important player to us and if Michael is fit, Michael will play."