"Like everybody else, we got it wrong," Tony Romando, chief executive of Topix Media, told The New York Post.
The edition appeared on shelves on Tuesday but was hastily withdrawn.
"All wholesalers and retailers have been asked to return any issues they have as we need to clear room for [150,000 copies of] the President Trump issue," said Mr Romando. "We expect it to sell very well as there is obviously a great demand."
He said only 17 copies were sold.
The front cover went viral as soon as it was publicised, with some Trump supporters - apparently oblivious to the alternative version - claiming it showed collusion between the mainstream media and the Clinton campaign.
Mrs Clinton was even spotted signing a copy at an eve of election event in Pittsburgh.
Mr Trump's shock win stunned even the network news journalists as they grappled with vote tallies late on Tuesday night.
America's leading professional association of pollsters has launched an inquiry into how they could the result so wrong.