"When a team is picked on the basis of colour they shouldn't be allowed to play. And that's exactly what's happening in Zimbabwe," the former Australian captain said during his current trip to India.
The International Cricket Council (ICC) is expected to debate Zimbabwe's future as a Test nation later this month following a revolt and subsequent sacking of the country's top 15 white players by the Zimbabwe Cricket Union (ZCU).
South Africa have already said they don't want to host a weakened Zimbabwe side and Cricket Australia (CA) have refused to rule out the possibility that it could press for the expulsion of Zimbabwe from Test cricket.
Waugh, who turns 40 on Wednesday, supported the decision to cancel Australia's recent Test series in Zimbabwe but said he would have been happier if the three One-dayers that followed had also been scrapped.
"I'm definitely happy that the Test series was deferred," he said.
"I think the players were uncomfortable with the situation. But I'm disappointed that the One-day series went on.
"The same logic that applied to the cancellation of the Tests applied here also. I'm a bit unclear as to why they played the One-day series."
Waugh's remarks were at odds with those of his successor Ricky Ponting, who said the decision to go ahead with the One-dayers was right.
"I've got no doubt it was the right decision," Ponting was quoted as saying after he returned to Australia on Monday.
"We went there to do our job, which is to play cricket. We didn't get involved in anything political but that's not saying we turned a blind eye."
Waugh, who retired in January as the second highest scorer in Test cricket behind compatriot Allan Border, also shot down Indian captain Sourav Ganguly's proposal to have a two-tier system for Test cricket to make it more competitive.
"It's a good idea for One-day cricket because there are more sides playing that, and they're looking to inject more sides all the time," Waugh said.
"For Test cricket though, I'm not so sure. There are only 10 sides, so if you split them up into two tiers the teams will get sick and tired of playing the same opposition year in and year out.
"I'm not sure how the teams in the lower tier will improve enough to move up.
"If you look at the history of Test cricket there have always been weak sides. Remember New Zealand took 26 years to win a Test match. I think we're getting a bit carried away because a couple of sides aren't doing too well."
The proposal to have a two-tiered system for Tests was mooted due to the lop-sided contests featuring the severely-depleted Zimbabwe and Bangladesh's inability to win a Test match since being admitted to the fold in 2000.
"I think Test cricket is in a pretty healthy state," said Waugh.
"The cricket that's being played at the moment is among the most aggressive that has been played in the history of Test cricket. There are results almost all the time and it's exciting."