If your job only requires BS +3 years experience and your company will post Job advertisements based on that you'll not be eligible for EB2. That'll qualify you for EB3.

Just because you have Masters Degree will not qualify you for EB2, the job that you'll be doing after you receive green card has to require Masters Degree.
If your company is willing to hire you for a future position that requires BS+5 years Experience or Masters Degree requirement then you'll qualify for EB2 category.

Therefore, if they want to file under EB2 category, the job requirement definitely will have to be different(BS +5 yrs or Masters Degree) than your current requirement (BS +3).

But, you can't count the experience that you have gained at the Green Card sponsoring company to meet that BS+5 yrs experience UNLESS the Future position is 50% different than your current position.
For example, if you are currently working as a software developer that usually requires BS+3 years experience..... but your company wants to file you under EB2 for different position (example: Sr. Developer or something) which requires more experience (BS+5 or Masters) then normally you can't show the experience you've gained at this sponsoring company. To count the experience that you have gained at this company then they'll have to prove that the duties for your future position: Senior Software Developer is at least 50% different than your current position (Software Developer).......

Since you have Masters Degree, if the Job description they post says BS+5 or Masters Degree then you don't have to worry about the experience part, then you'll qualify based on the Masters Degree.

Hope this helps !