Dear Mr.Mohan,
EPF online submission has been implemented since March paid in April 2012 by Indian government, all are compulsorily submit the contribution through online only surprising how your regional office accepting this?
Anyway there is software for EPF that you can download from EPFO website (DEMO file have attached for your reference) and you have to enter the required employee master then every month you need enter the employee wages and LOP details, the system will automatically generate the challan that you can directly upload thorough online. While entering the employee master and wages in the software no need to fill up individually you directly upload in the software by excel file in the .CSV format.
Payment you can pay thorough net banking
Regards
Sintralla