They really aren't.
I can see how he was confused - there is no US Commerce Agency or US Education Agency. Those are Cabinet level departments. The one entity he isn't going to make gone - teh EPA - that one's an agency (also Cabinet level!). It's what the A stands for.
Also too, eliminating the Department of Commerce kinda bones over the Census Bureau (an agency!). Teh census is constitutionally mandated. Why does Rick Perry hate teh Constitution?
UPDATE! Apparently there's a movie poster!