Two things need to happen to stop a query:
For the first point, the Oracle process that is executing the query should check from time to time if it should cancel the query or not. Even when it is doing a long task (big HASH JOIN for example), I think it checks every 3 seconds or so (I'm looking for the source of this info, I'll update the answer if I find it). Now is your software able to communicate correctly with Oracle? I'm not familiar with SLQ Navigator but I suppose the cancel mechanism should work like with any other tool so I'm guessing you're waiting for the second point:
Once the process has been notified to stop working, it has to undo everything it has already accomplished in this query (all statements are atomic in Oracle, they can't be stopped in the middle without rolling back). Most of the time in a DML statement the rollback will take longer than the work already accomplished (I see it like this: Oracle is optimized to work forward, not backward). If you are in this case (big DML), you will have to be patient during rollback, there is not much you can do to speed up the process.
If your query is a simple SELECT and your tool won't let you cancel, you could kill your session (needs admin rights from another session) -- this should be instantaneous.