If you were paying in SS while working for that employer then it shouldn't affect your benefit. Some federal, state and local government retirement plans exempt the employees from paying SS taxes. In those cases all you get is the pension, because you didn't pay into SS.
The current retirement system under the federal government is FERS, in which you pay a small withholding into the pension plan itself but unlike the old Civil Service Retirement System you also pay your full SS taxes. So when you retire you get a smaller annuity under FERS than you got under CSRS but you get the added benefit of collecting full SS along with it when you are eligible. Of course, we have the Thrift Savings Plan too so you really end up with three sources of income.
What Dandi said. The problem with the SS vs. pension thing is only an issue if your pension comes from a Social Security-exempt system, like the old Federal civil service system (CSRS). A LOT of state and municipal systems (Including teachers) are SS-exempt, and you are screwed under those (Of course, you aren't paying into it during your working life either, so there's that). But, the Fed civil service system that started in the 80s pays a much-reduced retirement but IS integrated into SS, so if you retire under it you collect both.
Where the REAL screwing comes is that if you qualified for SS under some other work history besides the exempt system, then qualified for a retirement pension under an exempt system (Say you worked 20 years for the city in an exempt system, but worked for the required 10-year minimum to qualify for minimal SS as a corporate employee paying FICA taxes), they still won't let you collect both, something I just found out about recently (Fortunately, it doesn't affect me personally).
