His England counterpart Alastair Cook insisted a "line had been crossed" after Sachithra Senanayake ran out England's Jos Buttler as the non-striker backed up at Edgbaston on Tuesday.
But Clarke said the dismissal was in the rules.
"At the end of the day I think as long as the player's warned it's obviously in the rules so you can make whatever decision you want," he said.
"Will an Australian player do it? I think I'd be silly to stand here and say, 'No, it will never happen under my captaincy'.
"At the end of the day it's in the rules."
Sri Lanka captain Angelo Mathews, asked by the umpires if he wanted to uphold what was a legitimate appeal, did not call Buttler back and the wicketkeeper was out for 21.
Sri Lanka went on to beat England by six wickets and clinch a 3-2 series victory.
Cook said he had never seen it before in a game.
"I was pretty disappointed with it to be honest with you. You don't know what you'd do if you were put in that situation, the heat of the moment, until you are. I'd hope I wouldn't do it," he said.
Even though 'Mankading', the term coined after India's Vinoo Mankad ran out Australia non-striker Bill Brown during the 1947/48 Sydney Test, remains a legitimate dismissal, some regard it as against the 'spirit of cricket'.
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