Waugh issued a scathing criticism of recent Test and One-day selections under Hohns and said his "confusing" strategy could lead to worried players focusing more on keeping their spot than contributing to a team performance.
"These decisions might spur the players to play for themselves rather than the team," Waugh said in a column in Melbourne's Age newspaper. "Hohns has done an admirable job but it might just be time to give someone else a go."
He was most scathing about Brad Hodge's "bizarre" axing from the Test team now in South Africa, even though he averages nearly 60 runs a Test and scored a double century against South Africa in the recent Test series in Australia.
Waugh rejected the selection panel's reasoning that Hodge lacked the batting technique and experience for such a tough tour and had not scored enough runs in the Australian domestic competition.
"It's the first time (domestic) form has counted so much with a player already in the Test team," he said. "The selectors didn't have a problem picking him with the same technique five games ago, so why is it a problem now?
"And why do we need more experience when four of the top seven batsmen have played more than 80 Tests (each)?"
Australia began the three-Test series against South Africa in emphatic style, winning the first match in Cape Town by seven wickets inside three days.
But Waugh said Australia had lost the One-day series in South Africa and last year lost the Ashes to England for the first time in 16 years, a defeat he said may have been partly due to the selectors' lack of faith in leg-spinner Stuart McGill.
"It might have been a different story if Stuart McGill had played in at least two of the five Ashes Tests," he said.
Waugh also cited the selectors' failure to play quick Brett Lee during the Test series in New Zealand last year and the decision to drop batsman Michael Clarke, who has since been reinstated, as examples of erratic selection.