The poll panel also served a show cause notice to another Assam minister for an alleged hate speech.
Expressing "displeasure", the EC warned Assam Food and Civil Supplies Minister Nazrul Islam and All India United Democratic Front MP Badruddin Ajmal to be "more careful" in their conduct in the future.
The EC said Islam had violated the provisions of the Model Code of Conduct by saying that "BJP is our religious enemy" and "everybody has to abide by Hindu code" while addressing a public meeting in Hojai on March 23.
It also rapped Ajmal for making communal and inflammatory remarks while addressing the media in Guwahati on March 22.
The EC quoted him as saying that "We will be guilty before Allah" if BJP is allowed to win even a single seat in Assam.
The poll body has also served a show cause notice to another Assam minister Himanta Biswal Sarmah for his alleged remarks in Tezpur on March 29 that "blood of Muslims" flows through pipes in Gujarat.
Assam polls: BJP, Cong face challenge to retain seats in third phase
Is corruption really an issue this election?
Assam: Modi, Rahul to hit campaign trail at same place on April 19
Kejriwal to file nomination from Varanasi today
Assam: Gaurav Gogoi's eligibility questioned