McGregor has re-joined the pool - where fighters must show clean doping tests prior to competing - for the first time since July 2021 after the Irishman broke his leg in a loss to Dustin Poirier.
The 35-year-old superstar was expected to face Michael Chandler later this year but is not allowed to fight until he has been in the testing pool for six months.
However, USADA were critical of the decision and revealed they were unable to confirm if McGregor would serve the full six-month period, with UFC officials and the Dublin native himself suggesting he could be granted a possible exemption in order to facilitate an earlier return to action.
"We can confirm that Conor McGregor has re-entered the USADA testing pool as of Sunday, October 8th 2023," said USADA CEO Travis Tygart in a statement.
"We have been clear and firm with the UFC that there should be no exception given by the UFC for McGregor to fight until he has returned two negative tests and been in the pool for at least six months.
"The rules also allow USADA to keep someone in the testing pool longer before competing based on their declarations upon entry in the pool and testing results.
"Unfortunately, we do not currently know whether the UFC will ultimately honour the six-month or longer requirement because, as of January 1st, 2024, USADA will no longer be involved with the UFC Anti-Doping Program.
"Despite a positive and productive meeting about a contract renewal in May 2023, the UFC did an about-face and informed USADA on Monday, October 9th that it was going in a different direction.
"We are disappointed for UFC athletes, who are independent contractors who rely on our independent, gold-standard global program to protect their rights to a clean, safe, and fair Octagon.
"The UFC's move imperils the immense progress made within the sport under USADA's leadership.
"The relationship between USADA and UFC became untenable given the statements made by UFC leaders and others questioning USADA's principled stance that McGregor not be allowed to fight without being in the testing pool for at least six months.
"Fighters' long-term health and safety - in addition to a fair and level playing field - are more important to USADA than short-term profits at the expense of clean athletes.
"USADA is proud of the work we’ve done over the past eight years to clean up the UFC, and we will continue to provide our unparalleled service to UFC athletes through the remainder of our current contract, which ends December 31st, 2023.
"As always, we will continue to uphold the rights and voices of clean athletes in all sport."
The UFC's next scheduled event is UFC Fight Night: Yusuff v Barboza on Sunday, October 15th and is headlined, followed by UFC 294 headlined by Islam Makhachev v Alexander Volkanovski a week later.
