The city's new police chief says the discrepancy came up in a review he ordered of the department's record-keeping systems.
The Examiner reports the analysis turned up about, on average, 100 more domestic violence assaults per month.
The paper reports other crimes apparently have been mislabeled as well, including robbery and burglary cases.
San Francisco Police Chief George Gascon says that fixing the problem will be one step in an overhaul of the department's computer system that could cost around $8 million.