If you say "it is being used" then it would imply that it's being used at this very moment. Its use began in the past, continues now, and extending into the future, although you don't know how far.
If you say "it has been used" then it has certainly been used in the past, and although it doesn't seem that it's being used at this very moment, it is certainly possible that it will be used again.
Examples like this are easier if you use real examples.
The microscope is being used by someone else right now. You will have to wait.
The microscope has been used by every student in the class and they all say it's their favorite part of science class and can't wait to look at something new next week.