Health issues and a heavy workload has seen the 47- year-old miss several one-day and Twenty20 series in recent years, including the just-ended limited-overs tour of India.
He returns to lead Australia in the upcoming Ashes series against England, but sees a time when there is one coach for Tests and another for ODIs and T20s.
"I think it will get to a stage where I'll probably have to look at changing that set-up," he told cricket.com.au.
Under Flower, England experimented with having a separate limited-overs coach, but the roles have since been combined again under Trevor Bayliss.
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Lehmann, who has coached Australia since 2013, said he would favour splitting duties between Tests and limited-overs, rather than having three coaches for the game's different formats.
"You can't split them three ways -- Tests, one-dayers and T20," Lehmann said.
"Some of the time there's no point another coach coming in, it's just logistical nightmares, so I think you'd probably go white ball, red ball."
The path is already well trodden by players, with many specialising in either Tests or ODI/T20s, although plenty still excel in both.
Lehmann said he could envisage the day when there were entirely separate XIs for each format.
"Cricket is really getting specialised. You can see a time when down the track... I don't know how many years but there'll be really significant changes and the XIs will be separate for each format or in red-ball and white-ball cricket," he said.
He acknowledged such a system could also problems, but insisted it was feasible.
"You've got big tournaments which are really important to win and your best side has to be available," he said.
"And there's always different stories, (such as) how (can) the young guys get an opportunity at the next level if you don't give them the opportunity when you get a chance?
"So there's pros and cons everywhere -- it's just how you balance it out.