'Flash Boys' Michael Lewis: Markets still rigged

Michael Lewis - Flash Boys

Controversial "Flash Boys" author Michael Lewis explains why the markets are still rigged and why complexity is the new opacity.

That said, he has one regret for using that word: It overshadowed everything else.

"My biggest complaint about the response in the book ... is the book generated this instant controversy and so once it became this object of controversy it didn't get read for what it was. It got seen as this provocation," Lewis said in an interview with " Power Lunch ."

In the book, Lewis claimed the market was rigged in favor of high-frequency traders, who use sophisticated computer algorithms to execute orders at very fast speeds.

The book sparked a heated debate about the merits of high-frequency trading.

Read More Why haven't 'Flash Boys' claims been proven?

Lewis said that it's not high-frequency trading that is inherently unfair, but the way the market is structured. The problem is that "distinguishing between good HFT and bad HFT is impossible."

He also thinks that the complexity of the market now allows for bad behavior to go unnoticed.

"I think it's generally true that complexity is the new opacity in the financial markets; that it's the way bad behavior gets disguised is it gets made very complicated. Complexity was at the root of the financial crisis," he said.

Read More Michael Lewis' 'Flash Boys,' one year on

Brad Katsuyama, the protagonist of Lewis' book and president and CEO of IEX, said Monday that despite the firestorm, most of the feedback he's received has been positive.

"What's been most surprising to me ... there was this real kind of intrinsic laserlike focus on high-frequency trading when in reality it was the system overall. It was about dark pools and HFT and brokers and exchanges," he said in an interview with "Power Lunch."

Last April, the infamous showdown between Katsuyama and BATS Global Markets then-President William O'Brien on CNBC stopped trading on the floor of the New York Stock Exchange.

Read More 'Flash Boys' claims 'a big lie': Bart Chilton

The fight kicked off after O'Brien accused Katsuyama of scaring investors to promote his business.

"It reflects ... a continued lack of understanding about how the market operates or just an unwillingness to acknowledge it because you're trying to launch a new business," O'Brien said at the time.

In response, Katsuyama reiterated his belief that the markets are rigged and told O'Brien, "You're a part of the rigging. If you want to do this, let's do this."

(To watch the full exchange, click here .)

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