Hi Ramakrishan,
Employee master data comes from multiple tables and also all data is time dependent hence overall data load for Employee takes a lot time. Below are some suggestions i have seen when we have seen same issue.
1) Load at non business hours as suggested by Suman
2) Divide load based on employee ID and then load then parallelly
3) Load master data weekly only when actual reporting is needed, HR reporting is not a daily reporting if reports need to be checked every monday load master data for Employee only on week-end.
4) We have finally done major improvement by moving architecture to Layered architecture and extract individual datasource and then stage it in DSO's. Integrate all source data based on time dependencies and then load into master data.
Issue is because of the design in which Employee master data is distributed in SAP.
Regards,
Ganesh