Apple spokesman Tom Neumayr said the Cupertino, Calif., company will appeal the order.
"Apple did not conspire to fix e-book pricing," he said. "The iBookstore gave customers more choice and injected much needed innovation and competition into the market. Apple will pursue an appeal of the injunction."
At trial, Apple insisted that its entry into the e-books market widened the number of customers and was a boost for publishers and authors alike, increasing the number of books available and eliminating a monopoly of the market by Amazon.com.
But the government argued that Apple joined with publishers to illegally undermine an Amazon pricing policy that had enabled consumers to buy the most popular books for $9.99.
In her order, Cote told Apple to make changes to its contracts with publishers to ensure price fixing is eliminated. She set rules to prevent the kind of cooperation she had cited between Apple and the publishers that she said harmed Apple's retail competitors in the e-book market.
For instance, she said Apple cannot enter an agreement with a publisher it had colluded with that restricts or limits Apple's ability to reduce retail prices or e-book discounts. And she said the company cannot put language in its contracts with publishers that tie e-book prices to those set by other publishers or retailers.
She said she will appoint an external compliance monitor for a period of two years to assess Apple's internal antitrust compliance policies, procedures and training and to recommend any changes necessary to improve them. She said the U.S., states that sued Apple and Apple can try to agree on a monitor to recommend to the court.
The order will remain in place for contracts between Apple and the various publishers until they begin expiring at six-month intervals in two years.
The judge also ordered Apple not to share the status of its contract negotiations with one publisher among other publishers.