Pay preparation - other than depending on their punching or an alternate way to monitor their attendance?

Dear Seniors, I work in HR of a Multispeciality hospital.Doctors are the hardest human resources to deal as they cant be controlled on the basis of strict rules like daily punching on time.We prepare the pay on the basis of attendance punching system and many of them have irregular punching, so i am not able to monitor whether they are present on every day or are they working for 9hrs.Maintaining attendance registers wont work in my organization. Can you please help me find out a way to prepare their pay other than depending on their punching or an alternate way to monitor their attendance?

Well, you can not force anyone to do the same either they are doctor or other professionals. Also, pointing them personally will also be not a good Idea.
What, I would suggest is to draft a common email mentioning the issue (don't point out anyone but keep it a general) and intimate them if the rule is not followed properly then strict action will be taken.
If the situation not improved send reminder for the same on fortnight or weekly basis. And finally at the end of the month you may take action by deducting salaries, issuing coc etc.
Also, if you are not using any HR or payroll software then go for it as it will help in managing employees very well in an easy way.. You can try SaralPayroll that comes with employee management as well as attendance management module that will help in monitoring employee attendance etc. Initially you can try its free or trial version.