The episode, which aired on June 1, saw Chopra's Federal Bureau of Investigation agent Alex Parrish thwarting a terrorist attack by Indian nationalists, who sought to blame the planned violence on Pakistan.
The producers said Chopra was not to be blamed for the episode as she did not have a creative control over it. Pee Cee took to Twitter to apologise.
Ms Chopra declared herself a "proud Indian" in a tweet and "extremely saddened" by any hurt caused by the show.
Though ostensibly planned by Pakistanis ahead of a summit about Kashmir, the disputed territory in the Himalayas claimed by India and Pakistan, Ms Chopra's character discovers it is in fact Hindu nationalists trying to frame the Pakistanis.
The Quantico episode that came under fire has received formal apologies from the network as well as the lead actor Priyanka Chopra, but some social media users can't help but await an apology for all the negativity that the Muslim population is hauled under by worldwide media.
Earlier, ABC Studios, the producers of the crime drama, have also offered an apology while defending Priyanka.
Priyanka Chopra posted a heartfelt tribute for her father Ashok Chopra's fifth death anniversary, on Instagram. The plot was deemed offensive by audiences, who then called for a boycott of Samsung, which features Indian actress Priyanka Chopra as a brand ambassador.
They continued: "Quantico is a work of fiction".
Bollywood diva Priyanka Chopra and her American TV series Quatico have been making headlines for all the right reasons ever since it first aired in 2015.
Quantico will wrap after season three, which is now airing.
'The show has featured a number of antagonists of many different ethnicities and backgrounds, but in this case, we involuntarily and regrettably stepped into a complex political issue. "It was certainly not our intention to offend anyone", the statement said.