There has been widespread calls for Clarke to move up the batting list from his usual position of five.
There has been no real consistency with the number three and four positions with Shane Watson, Rob Quiney and Ricky Ponting showing indifferent form and now the much-maligned Phil Hughes stepping into the role.
Thomson, who played 51 Tests for Australia, has called for the skipper to go up to three or four in the batting order to help protect his struggling teammates.
"He's got to go up one or two slots so these guys can have a little bit of protection," Thomson said.
"He's the in-form batter, he's seeing them like soccer balls sometimes and Clarke's got to listen to his own preaching.
"Clarke is not batting in the right position and is causing these blokes to bat out of position.
"He's got the most experience and he's got to front up to the bullets, were only playing Sri Lanka."
It was reported in The Australian that Clarke held a meeting with his top three yesterday and pleaded with them to lead from the front.
Clarke explained to David Warner, Ed Cowan and the new first drop, Hughes, the importance of good starts.
Thomson thinks Clarke needs to take responsibility as captain and move up the order.
"He's being doing this for a while," Thomson told radio station SEN.
"What about poor Punter who was going in before him and he was batting like Stevie Wonder and if he had half a heart he would have said, 'mate I'll go in before you and you go behind me and I'll protect you'.
"And when Punter got the flick he was sitting there crying and saying 'sorry to see my mate go'. Bullshit, what a lot of garbage that was."