Last month, work was paused after the skyscraper sunk another inch.
The city's request comes after a report found that the building's sinking is likely being caused by the construction.
VIDEO: Powerful winds blamed for shattering Millennium Tower window in San Francisco
A spokesman for the tower's management team confirmed that construction will remain paused until specific modification options are finalized.
As of February 2020, the building had sunk 17 inches since first opening in 2009.
RELATED: Could a building collapse like Florida happen in SF? UC Berkeley professor weighs in
Residents of the tower, located at Mission and Fremont in San Francisco, were first informed that the main tower was sinking in May of 2016.
Building representatives said last month that while there has been sinking and tilting, there has been no material harm to the building and it remains fully safe.