About 3,000 people had been evacuated and housed in temporary shelters as nearly 80 percent of Penang was hit by typhoon-like winds and heavy rain, its chief minister Lim Guan Eng said in a statement.
He said floodwaters had risen to 3-4 metres. Lim also warned in a Facebook post that more rain was expected and advised residents to stay at home.
Troops fanned out in Penang to rescue stranded flood victims and also to clear blocked routes and clean up.
Hundreds of trees were toppled and roads were submerged in Penang's historic capital of George Town, leaving many areas largely paralysed. The Malaysian state news agency said five people had been killed due to the floods.
"We remain fearful that there may still be untoward incidents because of the strong winds, the like of which have never been experienced before, and flash floods might recur," Lim told reporters in Penang earlier on Sunday, according to Bernama.
The Southeast Asian nation's meteorological service forecast stormy weather continuing in Penang as well as the neighbouring northern states of Kedah and Perlis.
An aerial view shows the banks of a river overflowed after floodwater rose for more than 24 hours of incessant rain, in Kubang Semang, Bukit Mertajam, Penang, Malaysia, in this still image from a video obtained from social media.
Flash floods caused by hours of torrential rain killed at least five people in Malaysia and military forces deployed on Sunday to help rescue thousands of displaced people in the northern state of Penang.
