Whenever I've come up against this question on an application form I've always ticked the YES box and then written at the side AFTER INTERVIEW.
If you don't reach the interview stage then there is no harm done with your current employer.
If you do reach the interview stage explain you are a caring, loyal employee and do not want to upset your current employer by having him/her thinking you want to leave.
Most references are only taken up AFTER someone has been offered the job.
Good luck. xx