Kunhalikutty, who defeated his nearest rival M B Faisal (CPI-M), won from all the seven assembly constituencies of Kondotty, Manjeri, Perinthalamann, Mankada, Malappuram, Vengara and Vallikkunnu by over 1,71,000 votes.
BJP candidate N Sreeprakash came third.
The bypoll was necessitated following the demise of E Ahamed, a former Union Minister and leader of IUML, a key partner in the Congress-led UDF Opposition in the state.
A former minister, Kunhalikutty is a member of the state assembly from Vengara constituency.
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The Election Office said that final declaration would be made after getting necessary clearance from the Chief Election Commissioner.
The muslim-dominated Malappuram is considered a bastion of IUML.
A total of 71.33 per cent voters had exercised their franchise in the bypoll against the 71.11 per cent recorded in the previous election here.
Of the total 13,12,693 electorate, 9,36,315 people including 4,93,433 women exercised their franchise.
In the 2014 Lok Sabha election, Ahamed had won the seat by a margin of 1,94,739 votes against CPI(M)'s P K Sainaba.