Hayes-White said 140 firefighters were spraying nearby buildings to prevent the blaze from burning other structures. She said there were no injuries.
"We are in a defensive mode," Hayes-White said.
"We are not quite contained, but we will be there a in few more hours," the fire chief said.
Some workers reported a scary, smoky commute home, and others took to Twitter to joke that the blaze might be an anti-gentrification plot.
The fire, reported just before 5 p.m., was burning in a neighborhood that includes office buildings, residential units and biotech firms.
Huge fire destroys Mission Bay construction project
A wall of flames engulfed a high-rise apartment building under construction in San Francisco's Mission Bay on Tuesday, sending black smoke thousands of feet into the sky as firefighters battled to keep the inferno from spreading to neighboring structures. Watch video and view more photos