Is it obligatory to deduct a portion of the salary equivalent to the times of leaving work to pray in the mosque or sleeping while performing a security guard duty for a government company, due to violating instructions?

Your work is security, and a private employee is obligated to perform the specified work on time. Exemptions to this are what has been established by custom or decreed by Islamic law, such as the five congregational prayers, Jumu'ah prayer, and times for rest, eating, and drinking. There is no need to stipulate this in the contract. However, if the employer stipulates to the employee that he should not go for congregational prayer, sleep, or eat during work, then the employee is bound to fulfill this condition.