Yes, it depends on the status of the person you are talking to. If they are "superior" to you in terms of age or position etc then typically in Japanese culture you shouldn't look at them in the eye. As you correctly noticed than when "subordinates" are talking to their boss or master they always look down at their feet and never make eye contact.
Having said that, you are not Japanese, so I'm sure a bit of friendly eye contact will not be misconstrued as anything negative. In my experience of working with Japanese people for several years, we always would make eye contact as otherwise (as you stated) it looks like you are not trustworthy or lying! Hope that helps.