The incident marks the latest in a series of abductions that have been blamed on the Abu Sayyaf militant group.
Armed men seized a fisherman off Malaysia's eastern coastline, an area where the Abu Sayyaf militant group has been known to kidnap people for ransom, an official said on Wednesday.
Earlier this month, three fisherman were also snatched inside Malaysian waters, by armed militants and taken to nearby southern Philippines.
The fisherman was snatched on Tuesday, the same day as two DAESH militants linked to the abductions of 26 Malaysian and Indonesian sailors were killed off a remote Philippine island. The details were not known.
"The attack was carried out by six suspects, some armed with M-16 rifles," Malaysian Marine police chief Abdul Rahim Abdullah said.
The Malaysian victim who owned the fishing vessel was with 20 other sailors when he was taken. Authorities did not say why he was targeted.
The Abu Sayyaf is a loose network of militants formed in the 1990s with seed money from Osama bin Laden's Al-Qaeda network that has earned millions of dollars from kidnappings-for-ransom.
Although its leaders have pledged allegiance to DAESH, analysts said they are mainly focused on lucrative kidnappings.