Voting in four polling booths in Kasargode and three in Kannur began at 7 a.m. and will end at 6 p.m.
As of 9 a.m., 20 per cent voter turnout was recorded the two constituencies.
Kerala had voted on April 23 to elect 20 Lok Sabha candidates. A few days later, there were visuals of people casting votes more than once was identified, prompting CEO Teeka Ram Meena to order the re-polls.
This is the first time in the state that a re-poll has been ordered.
Cases have been registered against the Communist Party of India-Marxist and Indian Union Muslim League workers, after identifying their members of voting more than once.