Pat Howard, who was appointed by CA in 2011 as high performance manager.
Howard oversees the controversial rotation policy and Warne said that Cricket Australia needs to put current cricket people in the administration of the game rather than involving people from other sports.
"I think CA really need to look at the people who are making decisions on all facets of cricket in Australia, we r seriously becoming a joke!" Warne wrote in his twitter page last night.
"Absolute rubbish re selections, rotations, resting & farcical decisions on matches, joke.. Dudding (cheating) the public & to(o) many excuses.. Wake up CA.
"Can CA please put current cricket people in charge to run the game, select teams, not ex rugby or any other sports people plse, seriously.
"We have the best batsmen/captain in the world in @MClarke23 (Michael Clarke) - He needs current cricket people to help him out not muppets," he wrote.
The 43-year-old reiterated his stand this morning but denied calling anyone 'Muppets' specifically and said he wants the best for Australian cricket.
"Morning all, read my tweets please & report correctly & responsibly, I never called anyone specific a muppett, don't assume, u may be wrong," Warne tweeted.
"Australian cricket is in disarray & in my opinion people are hoping Australian cricket will turn around Lack of a plan & a cricket strategy.
"As I said last night we need cricket people running the team & who understand cricket & what's required at the top level, not muppets!
"I am speaking as a frustrated Australian cricket team supporter & want what's best for Australian cricket," wrote Warne, who has claimed 708 Test wickets in his career.
Warne, who was fined a total of $9500 and suspended for one match during the just-cooncluded BBL season for various breaches of discipline, made the comments during Australia's two-run defeat via Dutchworth Lewis to Sri Lanka at the MCG in the second Twenty20 yesterday.
The Aussie great also promised to write "an in depth article on the state of Australian cricket" within the next 24 hours.
Former players, including Brett Lee and Ian Chappell, have criticised Cricket Australia's rotation policy, where players have been rotated in an attempt to avoid injuries, especially fast bowlers.
Australia's selectors had rested captain Michael Clarke, Matthew Wade, and David Warner for the first two matches of the ODI series after sweeping the Tests 3-0 against Sri Lanka.