Kaling starred in the US version of the show as well as serving as an executive producer, director and writer.
But she said the Television Academy, which oversees the Emmys, attempted to strip her of a producer's credit.
"I *was* singled out," she said. "The most junior person, and woman of colour. Easiest to dismiss."
Kaling played Kelly in the sitcom, and wrote and directed a number of episodes. She also found success with The Mindy Project, and recently starred in and wrote Late Night with Dame Emma Thompson, and wrote the Four Weddings and a Funeral TV reboot.
Her dispute with the Television Academy dates back a decade, when the organisation was trying to cut the number of producers credited on the Emmy nomination for each show.
The 40-year-old told Elle magazine the Academy forced her to go through a "humiliating" process to prove her contribution.
"They made me, not any of the other producers, fill out a whole form and write an essay about all my contributions as a writer and a producer," she said. "I had to get letters from all the other male, white producers saying that I had contributed, when my actual record stood for itself."
The TV Academy denied the process was personal and said "every performer producer and writer producer was asked to justify their producer credits".
An Academy spokesman told the Los Angeles Times: "No one person was singled out."
Kaling then took to Twitter to say their response "doesn't make any sense".
"There were other Office writer-performer-producers who were NOT cut from the list. Just me," she wrote.
"I worked so hard and it was humiliating. I had written so many episodes, put in so much time in the editing room, just to have the Academy discard it because they couldn't fathom I was capable of doing it all. Thankfully I was rescued by my friends, the other producers."
Kaling was listed in the nominations as a producer in the outstanding comedy series category in 2007 and 2008, and as a co-executive producer from 2009-11.
She noted the incident happened around 10 years ago and "maybe it wouldn't happen now" - however "it happened to me". Kaling has also asked the Academy to apologise.