by accepting the employment offered by the Company, through appointment letter, the employee and the employer enters an agreement.
The agreement ensures fair & just play for both employee and employer.
By not paying salary in time, which is one of the key conditions in the agreement (here appointment letter), the employer has breached the agreement.
Ideally on a legal perspective, the employee can send a notice to the company stating that due to...reason...you have committed a breach of the contract and necessary legal actions would be conducted to neutralize that..
OR at least ,
seek a written explanation as to why they have not been able to pay the employee in time...
However, if the employee chose to discontinue his/her service owing to this reason, and the company chooses to deduct the notice period from their arrears to be paid, that would a move in bad taste and could invite legal ramification...