The 70-year-old actress took to her social media page following the news that Caitlyn's E! reality show "I Am Cait", which followed her after she transitioned to become a woman from her former identity of Bruce Jenner, had been cancelled after two seasons.
"Now that @IAmCait has been cancelled, will she go back to being Bruce?" Midler had written.
The actress then added to the controversy by referring to Caitlyn's ex-wife Kris Jenner, and her ability to spin any experience into a money-making one, continuing: "Will Kris take him back? Do I smell a re-wedding?!"
"Dear friends @hrc, whom I have always supported," she wrote, referencing The Human Rights Campaign, America's largest civil rights organisation working to achieve lesbian, gay, bisexual and transgender (LGBT) equality.
"Sorry last tweet offended. An idle musing. I seem to have misread the temper of the times."
Midler's apology received a mixed response, with some accepting it and others suggesting the actress was still unaware of the major error she had made in her initial tweet.