International Trade and Industry Deputy Minister Datuk Mukhriz Mahathir said Japan was Malaysia's significant trade partner and had huge investments in the country.
"When a disaster of this magnitude happens, it will to a certain extent affect Japan's economic position and Malaysia too will feel the pinch.
"I hope the Japanese can restore the situation as quickly as possible so that the impact on the global economy is not that serious," he told reporters after the simultaneous opening of the Umno Youth, Wanita Umno and Puteri Umno branch meetings here Friday.
A powerful earthquake, measuring 8.9 on the Richter scale, struck downtown Tokyo at about 2.50pm, shaking buildings in the capital city for several minutes and forcing people out of their homes. Tsunami warnings were issued.
Many people rushed out of buildings, construction cranes atop buildings under construction swayed and some children were seen crying on the streets.
Train services stopped in Tokyo, long queues were seen at taxi stands, and power was cut off in some prefectures like Chiba and Ibraki.
Mukhriz said he did not know the fate of Malaysian companies operating in Japan and Malaysian students studying there.
The deputy minister said although earthquakes and tsunami were normal occurrences in Japan but "8.9 is a big figure. I pray all of them are safe...I also want to know what is their situation there."
As a close trade partner, Malaysia should extend whatever form of assistance needed by Japan to help ease the burden in the aftermath of the earthquake.
"If they need any form of help, we are prepared to send humanitarian mission," he added.
The aftershocks of the earthquake were felt by people in Labuan and Sabah and they have been advised to stay away from beaches due to rough sea conditions and high waves between 6pm and midnight.
The Meteorological Services Department said choppy waters were expected as the earthquake struck 4,434km north-east of Kudat in Sabah.
-- BERNAMA