"At the company level" would be something that affects the whole company, not just one particular part of it.

"At the site level" would be something that affects only one particular site, not the wider organisation.

"At the department level" would be something that affects only a particular department and doesn't affect the rest of the site or the company as a whole.

And so on. The phrase is used to limit or specify the extent of a described event or phenomena.