She allegedly told investigators the incident was a hoax meant to make them more marketable to the media.
"Mayumi described that she and Richard Heene devised this hoax approximately two weeks earlier.... She and Richard had instructed their three children to lie to authorities as well as the media regarding this hoax," the affidavit said.
Richard Heene has denied a hoax. His lawyer, David Lane, said Friday he is waiting to see the evidence in the case.
"Allegations are cheap," Lane said.
Mayumi Heene's lawyer, Lee Christian, was traveling and didn't immediately respond to messages left with his office.
Larimer County Sheriff Jim Alderden has said he will recommend charges against the Heenes including conspiracy, contributing to the delinquency of a minor, making a false report to authorities, and attempting to influence a public servant. The most serious charges are felonies and carry a maximum sentence of six years in prison.
Alderden said authorities also would be seeking restitution for the costs of the balloon chase, though he didn't provide a figure.
His office has said it will likely be next week before it forwards its findings to prosecutors to decide on charges.
In frantic calls to a TV station, 911 and federal aviation officials, the Heenes reported that they feared Falcon was in the homemade, saucer-like balloon when it was accidentally launched from their back yard last week.
Millions watched as media and National Guard helicopters tracked the balloon across the Colorado plains. It landed in a dusty farm field, where ground crews looked inside but found no sign of the boy.
Later, the relieved-looking couple reported Falcon had been hiding in their garage the whole time. But suspicion heated up when Falcon made a comment on CNN that sounded like "You had said we did this for a show."
Sheriff's deputies questioned the parents separately on Oct. 17, two days after the flight. Mayumi Heene told authorities "she and Richard Heene had lied to authorities on October 15, 2009 (the day of the flight)," the affidavit said.
She told investigators "that the release of the flying saucer was intentional as a hoax.... The motive for the fabricated story was to make the Heene family more marketable for future media interest," the affidavit said.
The Heenes twice had appeared on ABC's reality show "Wife Swap," and acquaintances said Richard Heene had plans for other possible shows.
The producer of "Wife Swap" had a show in development with the Heenes but said the deal is now off. The TLC cable network also said Heene had pitched a reality show months ago, but it passed on the offer.
Sheriff's officials declined to comment Friday.
Among the items taken by authorities during the home search were video cameras, computers, hard drives, a picture of a flying saucer, receipts, papers, a phone/address book and a flight itinerary. The list didn't identify the passenger, destination or date of travel.
Associated Press Staff Writer Kathy Packer contributed to this report from Fort Collins.