The National Weather Service is estimating waves in the Bay Area will reach heights of 2 to 3 feet, but waves as high as 8 feet are possible at Crescent City in Northern California, officials said.
San Francisco's Department of Emergency Management has activated the city's Emergency Management Agency and is accessing risk to coastal areas, department officials said.
No evacuation has been ordered as of 3:30 a.m.
The department is advising residents to monitor local media for updates.
The Coast Guard is putting out a broadcast to ensure that mariners are aware of the tsunami warning, a spokesman said.
They are monitoring the situation and will enforce a contingency plan if necessary, OS2 Kyle Jefferson said.
Officials in Santa Cruz, San Mateo, Marin, and Sonoma counties said they are continuing to monitor the situation but have not put into effect any emergency protocols.
The National Oceanic and Atmospheric Administration estimates that the tsunami could hit Point Arena at 7:26 a.m., Point Reyes at 7:39 a.m., Monterey at 7:44 a.m., and San Francisco at 8:08 a.m.
By the time it hits San Francisco the highest water is estimated to reach about two feet, National Weather Service forecaster Steve Anderson said.
But that is not just one little wave, but rather a surge of water, Anderson said.
Anderson said tsunamis usually occur in a series of surges and the coastal Bay Area could see three to five surges of varying sizes this morning.
Information on the tsunami's size will be changing throughout the morning as the tsunami approaches and more information is gathered.
The tsunami warning was issued for coastal areas of California and Oregon, from Point Concepcion in California to the border of Oregon and Washington, according to the National Weather Service.
The tsunami watch, issued shortly after midnight, was upgraded to a warning at around 12:45 a.m. and is expected to last through the morning, forecaster Will Pi said.
The tsunami was triggered by a 8.9-magnitude earthquake which struck the northeast coast of Japan late Thursday night.