"I know all the boys are looking forward to having him back and no doubt if I am unavailable ... I haven't spoken to the selectors but I would imagine that Watto would be captain," said Clarke, who is also a selector himself.
Watson, one of four players suspended for the third Test over the homeworkgate affair, was en route to Delhi on Monday after returning to Sydney for the birth of his first child.
Having been labelled a good team man sometimes by Howard last week, Watson is now facing the prospect of leading the side if Clarke is ruled unfit.
The latest twist in the Watson saga comes after the two-time Allan Border Medallist had called his ban harsh and claimed he was considering his playing future.
Watson now says he has had several constructive discussions with Howard after what Watson described as an emotional week.
Clarke's dual roles as skipper and leading batsman in the side would leave a gaping hole if he was absent and the 31-year-old is confident he can protect a proud record over his 92-Test career.
"It's pretty sore," Clarke said.
"Fortunately I have got a few days before the next Test and I will spend as much time with Alex (team physio Alex Kountouris) as I can to get it right.
"It is the same problem I have had since I was 17 and I have been trying to manage it throughout my career.
"The next four days will be no different to normal when my back goes on me like this.
"It's about plenty of treatment, listening to the experts and doing everything I can to get it right for the next Test match.
"Touch wood I haven't missed a Test match due to injury so far in my career and I wouldn't like this to be my first one."
