Doug Mills/The New York Times

The Justice Department jumped directly into the fight over the future of digital books on Wednesday — and Amazon came out the winner.

In an action that could lower the price of e-books and shift the expanding market in Amazon’s favor, the Justice Department slapped Apple and five of the largest book publishers with an antitrust lawsuit, charging that the companies colluded to raise the price of e-books.

The announcement, made in Washington by Attorney General Eric H. Holder Jr. and Sharis A. Pozen, the acting assistant attorney general of the Justice Department’s antitrust division, capped a long investigation. The inquiry hinged on the question of whether publishers, at the urging of Steven P. Jobs, then Apple’s chief executive, agreed to adopt a new policy in 2010 that in essence coordinated the price of newly released e-books at the price offered in Apple’s iBookstore — typically between $12.99 and $14.99.

At the time, Apple with its blockbuster iPad was trying to challenge Amazon’s hold on the e-book market. Amazon, the online retail giant, had become a kind of Walmart for the e-book business by lowering the price of most new and best-selling e-books to $9.99 — a price meant to stimulate sales of its own e-reading device, the Kindle.

Publishers, looking for leverage against Amazon, saw Apple as their white knight. The Justice Department complaint, using language that could have been inspired by a best-selling white-collar crime novel, describes how executives from the publishing companies met to discuss business matters “in private rooms for dinner in upscale Manhattan restaurants,” tried to hide their communications by issuing instructions to “double-delete” e-mails, all the time complaining of Amazon’s increasing influence over the e-book market.

Ultimately, the Justice Department charges, the publishers and Apple conspired to limit e-book price competition, increasing Amazon’s e-book retail prices and causing “consumers to pay tens of millions of dollars more for e-books than they otherwise would have paid.”

Three publishers that were investigated, the Hachette Book Group, Simon & Schuster and HarperCollins, have already agreed to a settlement that will most likely overturn their pricing model. Macmillan and Penguin Group USA, which were also named in the suit, have not settled.

For consumers, the suit and settlements could ultimately pave the way for lower e-book prices. The publishers who have settled are required to end their e-book contracts with Apple and any other retailer with a “most favored nation clause,” which says that no other retailer can sell e-books for a lower price. For two years, the publishers are also prohibited from restricting any retailer’s ability to discount e-books.

For Amazon, whose share of the e-book market has eroded to close to 60 percent from about 90 percent since 2010, the Justice Department action is a major victory over one of its top rivals, Apple. In anticipation of the announcement, Amazon already appeared poised to drop prices on e-books.

“This is a big win for Kindle owners, and we look forward to being allowed to lower prices on more Kindle books,” Andrew Herdener, a spokesman for Amazon, said in a statement.

An Apple spokesman declined to comment. A spokeswoman for Barnes & Noble, whose popular Nook reader helped it capture about 25 percent of the market after the new pricing plan wounded Amazon, said the retailer had no comment. Apple has about 15 percent of the market, several publishers said.

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The Justice Department investigation has set off worries among authors who fear Amazon’s huge influence over the market. Scott Turow, the president of the Authors Guild, warned in an open letter last month that the Justice Department was “on the verge of killing real competition in order to save the appearance of competition.” He added, “This would be tragic for all of us who value books, and the culture they support.”

According to the Justice Department lawsuit, the chief executives of the publishing companies met once every several months to “discuss confidential business and competitive matters, including Amazon’s e-book retailing practices.”

One of the meetings took place in the Chef’s Wine Cellar, a private room at Picholine, a Manhattan restaurant. One of the chief executives “reported that business matters were discussed,” the suit said.

“These private meetings,” the suit says, “provided the publisher defendants’ C.E.O.’s the opportunity to discuss how they collectively could solve ‘the $9.99 problem’ ” — that is, Amazon’s practice of charging $9.99 for most newer and best-selling e-books.

It was Mr. Jobs who suggested to book publishers that they sell e-books through Apple, with Apple taking a 30 percent commission — a strategy called the agency model. It was a significant switch from the wholesale model that publishers had been using for print books, under which publishers charged retailers about half of the cover price for a book and then allowed retailers to set their own sale price.

The five publishers made agreements with Apple for selling e-books, and Apple, which was about to introduce its iPad to the market, insisted on the “most favored nation” clause. That clause came under scrutiny by the Justice Department.

After making a deal with Apple in 2010, the publishers renegotiated their agreements with Amazon from wholesale to agency pricing. Amazon had little choice but to consent, though it would have preferred to keep e-book prices low.

In recent months, the Justice Department has sent publishers drafts of proposals that might form the basis of a settlement. The negotiations accelerated in the last several weeks as the department put more pressure on publishers to settle, according to people in the publishing industry with knowledge of the discussions. Ms. Pozen, who is expected to leave the department at the end of the month, was said to be determined to conclude the matter with either a settlement or a lawsuit by the time she left.

Even the publishers that finally relented did so reluctantly. HarperCollins said in a statement that while it had not violated any antitrust laws, the publisher “made a business decision to settle the D.O.J. investigation in order to end a potentially protracted legal battle.” Hachette said it “was not involved in a conspiracy to illegally fix the price of e-books, and we have made no admission of liability.”

John Makinson, chief executive of Penguin Group, said on Wednesday that his company had not held any settlement discussions. He added that the Justice Department document contained “a number of material misstatements and omissions, which we look forward to having the opportunity to correct in court.”

Macmillan released a statement maintaining its innocence. “The terms the D.O.J. demanded were too onerous,” said John Sargent, its chief executive. “After careful consideration, we came to the conclusion that the terms could have allowed Amazon to recover the monopoly position it had been building before our switch to the agency model.”

If e-book consumers stand to recover any money, it could come from the states. Sixteen states sued Apple and four publishers on Wednesday and have reached a settlement with two publishers.

According to the attorney general of Connecticut, George Jepsen, the price of an e-book was inflated by as much as $5 and the states thought the damages to consumers were more than $100 million. The publishers that have settled have agreed in principle to provide more than $51 million in restitution to consumers who bought e-books, Mr. Jepsen said.

In Europe, Apple and some of the same international publishers involved in the case in the United States made moves to settle a similar investigation with the European Commission. Apple was among companies to have made “proposals of possible commitments,” Joaquín Almunia, the antitrust chief for the European Union, said in a statement.

Many predictions about the effect Amazon would have on Apple’s success now appear exaggerated. As it was preparing to introduce the iPad, Apple initially saw having a competitive e-book offering as a critical to its new tablet device. By most estimates, digital books are only a small portion of its appeal.



James Kanter, Michael S. Schmidt and Nick Wingfield contributed reporting.