Mr Mukhriz Mahathir failed to secure the position of United Malays National Organisation (Umno) vice-president.
Defence Minister Hishammuddin Tun Hussein retained the vice-president's post when he beat Mr Mukhriz in a stiff race, reported Bernama.
Mr Mukhriz is the son of former Malaysian prime minister Mahathir Mohamad.
Mr Hishammuddin received 101 votes while Mr Mukhriz, who is Kedah Mentri Besar, secured 93 votes.
The other two vice-presidents are Home Minister Ahmad Zahid Hamidi (188) and Rural and Regional Development Minister Mohamad Shafie Apdal (177).
Dr Mahathir had expected that his son would not succeed in the contest. "I see that the same old faces got elected.
I told him (Mukhriz) that he will lose and had a 50-50 chance or less. My prediction came true," he said on Sunday.
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