The Straits Times reported that the boys parents, a mainland Chinese couple, were urged to secure their three-year-old in his seat moments before flight CX564 was due to take-off from Bangkok at 3:15pm on Tuesday.
However, the parents are said to have refused to do so and wanted the child to sit on his mothers lap instead, prompting an argument with flight attendants.
Hong Kongs South China Morning Post (SCMP) reported a passenger by the surname Lau telling Apple Daily that the boy had refused to sit down and wear his seatbelt.
A video taken by Lau showed another female passenger getting irritated with the commotion and asking the flight crew to call the police.
She was heard telling the Chinese couple in Cantonese: We are customers too. Why are you allowed to harass the whole flight?"
The toddlers father replied by saying they would not be bullied into leaving. If others keep harassing us, we will not leave the plane," he could be heard saying in the Putonghua dialect.
The family eventually left the plane grudgingly after more airline staff intervened in the commotion.
Cathay Pacific later told SCMP that the decision to remove the family of three was taken based on safety grounds, as the passengers refused to follow the cabin crews instructions.
The airline said the incident delayed the flight by almost 30 minutes. Just a day earlier, a similar incident was reported on a Hong Kong Airlines flight returning from Bali, Indonesia.
The flights crew were forced to call the police when a three-year-old boy refused to remain in his seat as the plane landed at Chek Lap Kok airport in Hong Kong.
The boys grandparent carried the boy despite the cabin crews insistence that the child should sit in his own seat and wear a seatbelt.