The government’s complaint “piles innuendo on top of innuendo.” It is based “entirely on the little circumstantial evidence it was able to locate.” And it “sides with a monopolist.”

These arguments were part of a response by two publishers, Penguin Group USA and Macmillan, to a Justice Department lawsuit filed in April that accused five major publishing houses of conspiring with Apple to fix the price of e-books.

Three of the publishers, Simon & Schuster, HarperCollins and the Hachette Book Group, denied violating antitrust laws but agreed last month to settle with the government.

Penguin and Macmillan, which declined to settle, filed responses in United States District Court in New York on Tuesday, not only denying that they had fixed prices but also taking direct aim at Amazon, the online retailer that has emerged as a significant threat to the longstanding business model for publishers.