Hi Nithin,
This can be managed with feature 'Attendance Regularization'. By this feature employees can raise a Regularization application and the attendance will take place on approval of the application. The Feature is available with only Lenvica HRMS Enterprise edition's ESS module.
You can see a demo of ESS from the link below,
ess.lenvica.in
To see the regularization module,
Location: ESS > Attendance > Regularization
Regards,
Rijo