Clarke denied playing a role in shutting down Katich's Test career, but following Australia's clinching of the one-day series against South Africa in Durban on Friday, the skipper said Katich's comments weren't conducive to team morale.
Clarke took over as captain from Ricky Ponting after the World Cup and became a selector when the Argus Review was handed down in August.
In Katich's comments, he suggested an infamous dressing room incident between he and Clarke at the SCG in 2009, where he grabbed the then vice-captain by the throat, impacted on his contract eventually being torn up.
'Look when Simon wasn't selected I wasn't a selector at the time,' said Clarke.
'Since becoming a selector I've made it clear in plenty of press conferences that I've done that the door's certainly not closed on anyone, but in saying that I don't think his comments are certainly helping him get back into this team at the moment.
'The team morale is such an important part of having success and it's been a great thing for the Australian team in both forms of the game of late.
'I think the team morale is outstanding and we're enjoying seeing a bit of success as well.' Also on Friday, Cricket Australia appointed a new full-time selector John Inverarity.
Clarke praised the decision but also paid tribute to the much-criticised outgoing head of selection, Andrew Hilditch.
'I'm very excited, (Inverarity's) the ultimate gentlemen, was a fantastic player and is a wonderful guy so I think both Watto (vice-captain Shane Watson) and myself are looking forward to spending a lot of time with him,' said Clarke.
'I think it's a great decision. 'I want to make a special mention to Andrew Hilditch. I think 'digger's' done a fantastic job and he's been a selector for a long time and I hope he's not just remembered for the last 12 months.'