BJP President Rajnath Singh along with other party leaders claimed that there were "nothing wrong" in Shah's statement. BJP leaders also claimed that it might be a case of political conspiracy.
Shah, during an election campaign rally in Muzaffarnagar, said that "this election is about voting out the government that protects and gives compensation to those who killed Jats. It is about badla (revenge) and protecting izzat (honour)".
There were nothing wrong in Amit Shah's statement: BJP defends Modi's aide
Shah, a close aide of Modi, was accompanied by BJP legislator Suresh Rana, an accused in the Muzaffarnagar riots. At least 60 people, mostly Muslims, had died, while thousands were rendered homeless during the communal clashes in Muzaffarnagar.
Both Congress and AAP complained to the Election Commission demanding strong action against Shah for delivering hate speech.
The Congress sought his arrest and asked the panel to ban him from campaigning for "creating animosity between communities" in western Uttar Pradesh.
The party also demanded "stern action" against the BJP and Modi, including derecognition of the party, for the alleged violation of the model code of conduct.
"BJP, Modi and Amit Shah are trying to replicate the politics of hatred and communal divide like what was done in 2002 in Gujarat," Congress spokesman Randeep Surjewala told reporters.
"We will make a demand to the state government and election commission that a criminal case is lodged against Amit Shah and Muzaffarnagar riots accused (legislator) Suresh Rana and they should be prevented from campaigning in any part of the country. There should be a complete ban (on them)."
The party said Amit Shah committed an offence under section 125 of the Representation of Peoples Act, 1951, which calls for the immediate registration of an FIR and his arrest.
The Aam Aadmi Party (AAP) also went to the poll panel, seeking action against the former Gujarat minister for spreading communal hatred.
"The EC should not allow such elements to create hatred at such a sensitive juncture, when the country is in the midst of a general election. The remarks openly incite people of one community to take revenge against another religious community and cannot be allowed to go unpunished.
"It should immediately order registration of a criminal case against the BJP's national general secretary Amit Shah for his inflammatory remarks aimed at spreading communal hatred," the AAP said in a statement.
(With agency inputs)