There was immediate backlash regarding the "The Blood of Romeo" episode of the popular drama, which stars Priyanka Chopra as former FBI/CIA agent Alex Parrish.
Chopra, who is Indian, is the first Bollywood actress to land a leading role in a prime-time American television show.
On Saturday, she tweeted an apology about the episode.
"I'm extremely saddened and sorry that some sentiments have been hurt by a recent episode of Quantico," the tweet read. "That was not and would never be my intention. I sincerely apologise. I'm a proud Indian and that will never change."
ABC had earlier issued a statement in response to the criticism.
"ABC Studios and the executive producers of Quantico would like to extend an apology to our audience who were offended by the most recent episode, 'The Blood of Romeo.' The episode has stirred a lot of emotion, much of which is unfairly aimed at Priyanka Chopra, who didn't create the show, nor does she write or direct it," the statement read. "She has no involvement in the casting of the show or the storylines depicted in the series."
The statement went on to add that "'Quantico' is a work of fiction."
"The show has featured antagonists of many different ethnicities and backgrounds, but in this case we inadvertently and regrettably stepped into a complex political issue," the statement concluded. "It was certainly not our intention to offend anyone."
The storyline of the episode, which aired June 1, revolved around a plot hatched by Hindus ahead of a summit and angered many fans.
"That entire episode was not just an attack on Hindus but also an attack on India," one person tweeted. "Peddling Pakistani agenda that Indians make elaborate plots to frame Pakistan. Shame on @priyankachopra for even thinking such a storyline was acceptable."