do we now have to pay for our employers super and pay medicare before tax and after tax?

my end of year payslip states that i recieved x dollars and paid so much in tax when you add up the normal time pay and the holiday pay and sick pay it comes to roughly the ammount that it states i get per year . but on my tax form from them it has a higher amount than the pay slip. when i queried this i was told that it was because of medicare and super. my question is how?