How you handle a situation where there is a conflict of interest between you and your Boss in an office environment?

First of all, there should be a declaration for any kind of conflict of interest from all employees in the organization.

Then and according to the type of interest and up to what level conflict with the company standard and policies, there should be and action that eliminate this conflict.

In my opinion,  HR should not at any way, to compromise company policy in this regards.

There is a need to know which of you have interests that are in-line with the goal and objectives of the organization. If, your goal and motives serve overall organizational goals and your supervisor tells you to do otherwise then there are two things that you can possibly do.

1. Brief your supervisor about how his directives will go against the objectives of the organization. You can do that by elaborating organization vision, mission statement and general rules and regulations.

2. In case, even after your explanation, he/she directs you to go against organizational objectives, then you should simply keep the top management of the company in loop.