Employer Can Deny An Employee To Sign Attendance Register After Unauthorised Leaves?

Whether an Employer can deny an employee to sign attendance register if the said employee wants to report for duty after being remaining unauthorised absent for some days?

That will be violation of the following acts as the intention is clear that he will not pay you for that day :-
1) Factory Act
2) Payment of Wages Act
3) Minimum Wages Act
4) Shops and Establishment Act & any other law effecting wages as PF and ESI of that day is also not paid wrongly.
You can simply contact area labour inspector and lodge a complaint. Ask him to keep you anonymous. That is your right so he will issue a show cause without name of complainant.

Unauthorised absence is a punishable misconduct on the part of an employee for which the employer is empowered to initiate disciplinary action separately if he so desires apart from with holding his salary for the period of absence. However, he can not prohibit or prevent the employee from signing attendence when he reports for duty unless the employee stands already suspended for it would amount to denial of employment.