Mohd Zubil Mat Som, a local official of Malaysian Maritime Enforcement Agency (MMEA), said a fisherman found the vessel after his fishing net was entangled with its engine, according to a report by Bernama, the state news agency.
Mohd Zubil said one of the engines had been retrieved, adding that the brother of its owner, who remains unaccounted for, verified it as coming from the missing boat.
He said the search and rescue operation would focus on locating the victims.
The four people, including one Chinese, two Spanish tourists and a local went missing on May 2 when they travelled on a speedboat in Sabah Kudat area but failed to arrive at the destination.
Chinas Consulate-General in Kota Kinabalu, the state capital, confirmed to Xinhua that the missing Chinese citizen was from Chinas Hong Kong Special Administrative Region and was operating a vacation resort in Sabah.