A water spout was seen over the waters near Johor Baru.
It seemed to be moving in the direction of Tuas, said a witness.
The netizen, Mr Lim, sent in photos of the sight to citizen journalism site Stomp.
He said the water spout took around five minutes to move.
A water spout is a funnel-shaped vortex over water.
It is connected to a cloud and is usually weaker than its land counterparts such as tornadoes.