The phenomenon was recorded around 9.30am, and is believed to have occurred in waters off Kg Mampakad and Kg Rosob.
Videos of the waterspout went viral on social media and messaging apps.
Users commented with messages saying it was "scary" and called for others to "be careful" and "pray for our safety", among others.
Sabah Fire and Rescue Department officials said there were no reports received over the waterspout but they would be on standby for any eventuality.
Sabah Meteorological Department director Amir Zudi Hashim said they were unable to verify whether the phenomenon was recorded on Friday and at the mentioned location.
Last month, a landspout struck parts of Ipoh and caused extensive damage to houses.
Earlier, it was reported that The Malaysian Meteorological Department's Centre for Meteorological Instrumentation and Atmospheric Science senior director Ambun Dindang said several states on the west coast of the peninsula as well as Sabah and Sarawak, could possibly experience landspouts (or waterspouts) as well.
He also said they tend to strike coastal areas such as Bintulu and Miri in Sarawak, Labuan and western Sabah.
Ambun added that it was quite challenging for MetMalaysia to forecast landspouts as they tend to occur on a smaller scale and have short lifespans of an hour, at most.
He said they can, however, monitor cumulonimbus clouds through radar images throughout Malaysia, as these heavy clouds are the early signs of the mini-tornados.
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