Check the datasheets for your part, but it is generally not a good idea.
Some parts will allow it in some cases for example a 2.5v signal to drive a 1.8v io standard pin (some of the Altera stuff IIRC), but you want to be very careful with 3.3v stuff (and watch out for overshoot and ringing, fpga pin buffers are more then fast enough for this to be an issue).
Note that this also depends on exactly how you have configured the IO pin, sometimes clamp diodes are optional and sometimes you can get away with it with sufficient series resistance, the data sheet will reveal all.
Regards, Dan.