Reports that DC had cancelled production on the film, in which Gal Gadot was set to reprise her role as the super heroine, emerged earlier this week.
It comes as Marvel's Guardians of the Galaxy director James Gunn, who has taken the helm of DC, said his first month of restructuring the franchise had been "fruitful", but that he and his team were "just beginning" their work.
In a lengthy statement on Twitter, Jenkins acknowledged that the franchise was "buried in changes" and that difficult decisions had to be made.
"When there started being backlash about WW3 not happening, the attractive clickbait false story that it was me that killed it or walked away started to spread," she wrote.
"This is simply not true. I never walked away. I was open to considering anything asked of me. It was my understanding there was nothing I could do to move anything forward at this time.
"DC is obviously buried in changes they are having to make, so I understand these decisions are difficult right now."
She added: "I do not want what has been a beautiful journey with WW to land on negative note. I have loved and been so honored to be the person who got to make these last two Wonder Woman films.
"She is an incredible character. Living in and around her values makes one a better person every day. I wish her and her legacy an amazing future ahead, with or without me."
Jenkins went on to praise Gadot and actress Lynda Carter, who played the role of Wonder Woman in the original 1975 series, describing her as "an absolute legend and beacon of goodness and light".
She also thanked Wonder Woman fans for their "love and support", telling them they were "first and foremost in our minds every day we made the last two films".
"Wonder Woman fans are often not the most visible in the media and online, but I want you to know that we have always seen and celebrated you and your importance."
Gunn responded to Jenkins's Twitter post soon after, saying "I can attest that all of Peter and my interactions with you were only pleasant and professional."
Gunn and Peter Safran were hired to lead the DC Extended Universe and have been working together to create a presentation that shows Warner Bros Discovery chief executive David Zaslav what the franchise's future schedule will be.
Jenkins rose to prominence with her 2003 film Monster, which earned Charlize Theron a best actress Oscar.
She went on to become the first female director of an American studio superhero movie with the first instalment of Wonder Woman in 2017.
The first Wonder Woman film opened to critical acclaim and earned $822.8 million at the box office. Wonder Woman 1984, which was released in 2020, received mixed reviews and made $169.6 million in cinemas.
On Tuesday, Gadot tweeted a “thank you” to fans, sharing that she “can’t wait for the next chapter".
“A few years ago it was announced that I was going to play Wonder Woman. I’ve been so grateful for the opportunity to play such an incredible, iconic character and more than anything I’m grateful for You,” she posted.