what does the phrase "at a site level" mean?

Question

for example:
1.At a minimum, a checklist of things to address at a site level should be made available for those participating.
2.The design, or exemption, at a site level can be approved if both of the following criteria are met.
3.Information that can be maintained at a site level.

Answer 1

The phrase "at a/the --- level" generally is setting a frame of reference. So, "at a site level" means "in the frame of reference that refers to a specific site in question," as opposed to at the corporate layer above or below the site itself.
If one says, "at the store level," then he or she is referring to actions made in the stores, as opposed to at the district or corporate office.
So, to rephrase your three points:
1. a checklist referring specifically to the site itself
2. the design or exemption referring to the site itself
3. information that can be kept and recorded on the site itself

Answer 2

I am guessing from the information you have given it means a participating location.

a site is a location or random origin.