Kondabolu said the character and his thick Indian accent was based on hurtful stereotypes.
"Everything with Apu is like this running joke," Kondabolu told the New York Times. "And the running joke is that he's Indian."
Earlier this year, The Simpsons addressed the racial controversy surrounding the character in a brief scene of an episode that was described as a "slap in the face."
The show producers slipped in a scene with Lisa and Marge Simpson, who is reading an updated version of The Princess in the Garden that was edited to make it acceptable for 2018.
At one point, Lisa turns to the camera and says: "Something that started decades ago and was applauded and inoffensive is now politically incorrect. What can you do?"
Lisa then looks at a picture of Apu with the catchphrase "Don't have a cow!" written on it.
"Some things will be dealt with at a later date," Marge says.
"If at all," Lisa responds.
The episode attempted to bandaid the issue but was met with further controversy.
Shankar views the decision to axe Apu as a mistake, saying: "If you are a show about cultural commentary and you are too afraid to comment on the culture, especially when it's a component of the culture you had a hand in creating, then you are a show about cowardice."
"It's not a step forward, or step backwards, it's just a massive step sideways."