Although descriptive words are usually applied to it to simply describe an organization or company, I'd say it can still be used synonymously with the word company. This would be a secondary usage and not as common as the first way I spoke of.
It's not a direct synonymfor the word "company". However, it could be used that way.
This is what I thought. The various definitions provided by OneLook bear this out.
Atomica says it is "a business organization" as a secondary definition. A business organization, to me, would be the same as a company.