Last week, Justice outlined its proposed remedies against Apple.
The government asked the court to force Apple to terminate its agreements with the e-book publishers and to bar the company from entering into similar agreements for five years. The restriction would also apply to Apple's negotiations with suppliers of music, movies and television shows.
Under the proposal, the court would appoint an external monitor to examine Apple's business practices to ensure they are not stifling competition. The company would also have to hire an internal officer to conduct audits and train senior executives about antitrust laws.
Apple would have to allow Amazon, Barnes & Noble and other e-book retailers to provide links from their e-book apps to their online bookstores. The feature, which would be mandated for two years, would allow consumers to easily compare prices, the Justice Department said.
Apple has called the proposal a "draconian and punitive intrusion" into its operations.
In their filing, the publishers argued that the proposal would limit their ability to strike agreements with Apple, effectively modifying the settlements they already agreed to with the government.