Lewis' book, released last spring, led to considerable debate over high-frequency trading, which uses computer algorithms to carry out swift orders. In an afterword written for a paperback version set for release next week, he contended that "the entire system," not just high-frequency trading, was to blame.
"The big banks and the exchanges have a clear responsibility to protect investors-to handle investor stock-market orders in the best possible way, and to create a fair marketplace. Instead, they've been paid to compromise investors' interests while pretending to guard those interests. I was surprised more people weren't angry with them," Lewis wrote in the afterword, which originally appeared as a Vanity Fair essay.
He suggested that a tilted market persists despite regulator action against some Wall Street institutions since the book's release.
Chilton criticized high-frequency traders as "cheetahs" during his time at the Commodity Futures Trading Commission.
He left the CFTC last year and now works with high-frequency trade association Modern Markets Initiative in his job at law and lobbying firm DLA Piper. He called Lewis' claims "irresponsible," arguing that academic research has debunked them.
Chilton said that the United States needs more "simple markets" with "more transparency." However, he contended that high-frequency trading is "part of our markets today," saying that "front running," trading on analyst information before the client receives it, "cannot be done" by high-frequency traders.
In a statement to CNBC, Lewis contended that investors get better results when using exchanges with technology designed to prevent front running. IEX, the exchange outlined in "Flash Boys," uses such technology, he said.