There is a simple workaround for this problem. Any way you got these three names printed in your PAN. Out of these three names, surname is the mandatory one you need to enter in the online registration process while other two are optional. To find out which is the surname that you had given in the application out of these three names, check the fifth(5th) character of your PAN, since it is the first letter your surname. Suppose, if it is ‘M’, the name which starts with the letter ‘M’ has been given as surname in the pan application form.
If you get your surname, you can easily find out other details (First Name, Middle Name, etc, ) by using this page : Know Your PAN
Source : http://www.gconnect.in/personal-income-tax/how-to-solve-first-name-surname-confusion-while-registering-pan-for-online-itr.html