The mess figures to hurt the former San Francisco 49ers star's chances of returning to the NFL for the first time since 2016, even though 25 clubs had sent representatives to watch Kaepernick's session.
The NFL had planned a private workout at the Atlanta Falcons training facility, but Kaepernick representatives said about 30 minutes before its scheduled start that he was instead moving the workout to a nearby high school and postponing the start.
A statement from representatives of Kaepernick said he was concerned about "an unusual liability waiver that addresses employment-related issues" that the NFL wanted him to sign and that he wanted media to be able to observe and film his workout.
The NFL planned to videotape the event so all 32 teams -- not only the 25 who sent player personnel executives -- would have access to Kaepernick's performance, which would include throwing to receivers and other quarterback drills.
The NFL, in a statement, expressed dismay that Kaepernick skipped the planned session.
"We are disappointed that Colin did not appear for his workout," the NFL statement said.
"Today's session was designed to give Colin what he has consistently said he wants -- an opportunity to show his football readiness and desire to return to the NFL."
Kaepernick was an NFL star in 2016 when he began kneeling for pre-game playings of the US national anthem as a way of protesting racial inequality and social injustice. He opted out of his 49ers contract for free agency in 2017, but found no takers.
Later in 2017, US President Donald Trump began attacking NFL players who kneeled for the anthem, saying they should be fired and calling any such player a "son of a bitch."
Trump painted the protest as an insult to the flag and the nation rather than the issues Kaepernick had championed.
Kaepernick had reached a settlement with the NFL over claims that owners were improperly keeping him out of the league when many teams over the past three seasons have needed a top passer due to injury or futility.
The NFL workout session was seen as a way to open the door for clubs to show interest without any team having to bear any possible criticism over bringing in Kaepernick for a tryout.
"The NFL made considerable effort to work cooperatively with Colin's representatives," the league statement said. "We invited his agent to suggest questions for the interview.
"Yesterday, when Colin's representatives said he wanted to bring his own receivers to the workout, we agreed to the request."
Former Cleveland Browns coach Hue Jackson was brought in to oversee the session and spoke with Kaepernick's agent about exactly what drills would be run to he would know what to expect.
Jackson did not take part once the location was moved, a posting on the NFL's website said.
Kaepernick sending film
The league also said it agreed to a request by Kaepernick that Nike be able to shoot an advertisement featuring him and mentioning every NFL team that attended the workout.
Kaepernick's representatives told the NFL Network they plan to film the quarterback's open session and send the video to every NFL club.
Kaepernick attorney Ben Meiselas and agent Jeff Nalley told ESPN in a statement their client wanted "a transparent and open process, which is why a new location has been selected."
"From the outset, Mr. Kaepernick requested a legitimate process and from the outset the NFL league office has not provided one," the statement said.
"The NFL has demanded that as a precondition to the workout, Mr. Kaepernick sign an unusual liability waiver that addresses employment-related issues and rejected the standard liability waiver from physical injury proposed by Mr. Kaepernick's representatives."
The failure to have an NFL-sanctioned workout session keeps Kaepernick a free agent with no offers.
"Colin's decision has no effect on his status in the league," the NFL said. "He remains an unrestricted free agent eligible to sign with any club."