Jo Puccini, who runs the investigations and current affairs department at the ABC, resigned on Thursday.
In an email to all staff, acting ABC news director Donna Field said she wished Puccini "every success in whatever comes next".
"Jo has helped shape significant public interest journalism and built high-performing teams, leading to numerous Walkley awards," she said in the email viewed by AAP.
A statement in the email attributed to Puccini said she had pride in the journalism she had produced.
"It's been an adventure and a privilege to work at the national broadcaster, an institution where I've made lifelong friends. It's now time for a new chapter in my career," she said.
Puccini has faced a backlash for overseeing the work of bikie-turned-journalist Mahmood Fazal, who worked on Four Corners.
Concerns were raised by the ABC's Media Watch program about the veracity of sources he used in two programs aired during 2023 and 2024.
Two episodes of Four Corners, Cocaine Nation and Meth Highway, were removed by the ABC due to accuracy concerns.
In both episodes, a masked figure who purportedly dealt cocaine to Sydney's elite was featured.
Media Watch later reported Sydney-based rapper Charissa Habkouk played the role as a favour to Fazal.
A Background Briefing audio program Fazal worked on was also removed.
His employment was terminated in 2025 after an ABC investigation into his appearance on a podcast with a former underworld figure.
It is not suggested Puccini knew about or was involved in any wrongdoing surrounding the episodes.
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