The Rambam discusses at length the responsibilities of an employee to avoid any form of stealing in the workplace. Clearly, one is prohibited from using office supplies and materials, such as stamps, for personal benefit. Moreover, one must scrupulously avoid taking work time for personal tasks. For example, if someone punches in to work at 9:00 am, but then proceeds to pray Shaharit, that prayer is considered personal time and is taking away from the employer. After all, he Is not being payed to pray. Therefore, he should first pray and then punch in.
While it is true that the Gemara states in Masechet Berachot that workers are permitted to pray on the job, that is referring to a case where the employees work from dawn until nightfall. There was no possibility to pray before work, and therefore, it was considered part of the job description. Today, a person has from dawn until 9:00 to pray. The fact that he was late is not an excuse to pray on the employer’s time.
There is another Halacha which people don’t understand. They think that they are permitted to leave work in the middle of the day to go pray Minha with a Minyan. The Poskim say that Tefilot must be done on his own time, such as a lunch break. Praying by himself without a Minyan is certainly better than praying with a Minyan on his employers account. Today, with the advent of Minyanim in the office, it is less of a problem.
Clearly, there is no justification for a person to sit and learn for a few minutes after the prayers on his employer’s time. Over the course of a year, these few minutes add up to stealing days of time from the employer.
The best course of action is to reach an understanding with the employer and gain his consent for prayers during the workday or use of office supplies. The fact that "Everyone is doing it," is not an excuse. This recalls the biting lament of the Ya’abets who noted that people are often more scrupulous in observing Minhag than the actual law. He commented that it is unfortunate that "Lo Tignov" (Though shall not steal) is not a mere custom, because then, everyone would keep it. But, unfortunately, it is "only" one of the ten commandments.
One may not take work time to pray or learn without the employer’s consent.