Waite is still nursing a knee injury suffered in the Blues round 15 loss to Collingwood, but is expected to push for selection within the next fortnight.
His availability has suddenly created headaches for Malthouse, who is hesitant to substitute Waite for Lachie Henderson up forward.
Henderson has kicked 11 goals in Waite's absence, and Malthouse told SEN radio of his new role for Waite.
"Jarrad has played a lot of football in the backline.
"I'm reluctant to say that they both will play together in the forward line, because I think that you've still got to have that structure where you can have a ruckman on the ground.
"When your league ruckman, if you like, spends a couple minutes in the forward line and then goes to the bench you've still got to have a ruckman.
"Jarrad or Lachie, neither of these blokes are ruckman.
"The structure will change. Sometimes when things are working, you get a bit reluctant to actually change up.
"There's a little bit of work to be done with those players playing together."
Malthouse indicated the club would be active in the off-season as it looks to make changes to its playing list.
"Our list will be cut. How deep is still to be debated," he said.
"What we've got to do is weigh up what can take us forward. Do we release players to go forward, and that will be probably the case. How many is still unknown.
"You look at what other sides cut. One man's rubbish is another man's treasure. We've got to look at it and see if someone there can fit in."
