FMLA and the CA close equivalent the CFRA provide you with 12 weeks of leave. Once that 12 weeks concludes, you still have certain rights to leave under the Fair Employment and Housing Act that need to be considered. Under that law, your employer is required to engage in an interactive process to see what can be done to accommodate your temporarily disabling condition. One way an employer can reasonably accommodate an employee with an injury like yours is to grant additional finite leave to allow you to complete your healing and rehabilitation. The employer is required to do that if it will not create and undue hardship on the employer.
It is important that when your doctor provides a status update on your condition that there be an estimated return to work date. It might be two or three months down the road, and it may get extended further at that point, but there needs to be a return to work date that is not so far out as to render the leave to be an undue hardship.
Good luck to you.
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Your initial post and the follow-up you provided after Mr. Pedersen's response need some clarification. What kind of disability are you asking about? There is California State Disability Insurance (SDI), Social Security Disability Insurance, workers' compensation temporary or permanent disability – which could be total or partial, short-term or long-term disability under an employer-provided insurance plan, or your own insurance plan.
FMLA is federal law, and the California Family Rights Act (CFRA) is a California law. Both allow an employee with a serious medical condition a leave of absence from work, after which the employer must return the employee to the same or substantially similar job. The amount of leave must be 12 weeks or less, and can be taken intermittently in any increment, even as small as one hour, as long as the total does not exceed 12 weeks. Please look at my Avvo guide on the Family and Medical Leave Act, 29 U.S.C. section 2101 et seq. (FMLA): http://www.avvo.com/pages/show?category_id=6&permalink=family-and-medical-leave-fmla-summary-of-key-provisions.
If you are on FMLA and your medical status changes so that you now qualify for something other than, or in addition to, FMLA, there is no logical reason you cannot pursue whatever other options you have. Still, without knowing more details, it's impossible to discuss your situation.
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The employer is most likely incorrect. Besides FMLA/LOA, you might be also entitled to additional leave as a reasonable accommodation to your injury/disability and possibly other accommodations. It is important to bring this to your employer's attention before they take action against you, such as terminating you, as that would be in violations of disability laws.
San Francisco Employment Lawyer