Can my employer deduct anything from my paycheck if I come to work late?

Yes, your employer can deduct money from your paycheck for coming to work late. The deduction shall not, however, exceed the proportionate wage that would have been earned during the time actually lost, but for a loss of time less than 30 minutes, a half hour’s wage may be deducted. Labor Code Section 2928.  

For example, if you earn $12.00 per hour and come to work 40 minutes late, your employer can deduct $8.00 from your paycheck. And if you come to work five minutes late, your employer can deduct $6.00.

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