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"Donald is 180 degrees wrong," Cuban told CNBC's "Squawk Alley" by phone.
In a Reuters interview, Trump said technology start-ups that had never earned a profit were able to sell shares at very high price. He likened the situation to the overheated stock market in 2007.
"I'm talking about companies that have never made any money, that have a bad concept and that are valued at billions of dollars, so here we go again," the New York tycoon told Reuters.
Cuban, a tech entrepreneur and owner of the Dallas Mavericks, said Trump's comments make it sound like there's a bubble in the public markets, which isn't true.
"That's 180 degrees wrong because none of those companies are going public," the "Shark Tank" host said.
"If we have a problem, it's not that there's frothy valuations for tech companies in the public market. It's that there's no tech companies that have high growth rates that are in position to get frothy valuations. That's the problem," he said.
Cuban said the recent slowdown in IPOs of tech companies is only hurting the economy, and he criticized Silicon Valley's current ethos of not going public.
"By not going public, we are creating significant issues in the economy, significant issues in the market. It's a real problem for all of us," he said. "If companies don't go public, you create more power for the incumbent or legacy companies that are already public."
Cuban added that if people are looking for a bubble in tech, it may be in private companies.
"In terms of the private tech investments, there's certainly a bubble. ... So while we're not in a bubble like we had in 2000 — I mean it's not the same at all because we're talking about private companies — for private investments, you are stuck," Cuban said.
"If you make an investment in a private company today because of the culture, particularly in Silicon Valley, that says you should not go public, you need to write down that investment to zero immediately because you have no liquidity. Whether or not you want to term that a bubble, that's up to you, but it's not good for private investors right now," he said.
Many tech watchers have repeatedly warned of a tech bubble as the number of private companies valued at $1 billion or more — known as unicorns — have soared to 163, according to venture capital research firm CB Insights.
Cuban said even though Trump is wrong, the presumptive Republican presidential nominee's comments won't hurt his chances in November.
"It helps him with his tribe. The people who follow Trump, they're not looking for substance and he's smart not to provide them," Cuban said.
— Reuters contributed to this report.
Disclosure: CNBC owns the exclusive off-network cable rights to "Shark Tank."