Using internal pull-ups for TWI on AT32UC3B?
The question is not "can" you use them, but "should" you use them.  If it does happen to be the case that you can use them, should you actually use them?

Given that the internal pullup resistors are typically 10-50x larger than the values you should use on an I2C bus, the answer is a resounding "NO!", and Arduino are criminally insane for suggesting that you do (and indeed enabling them by default).