Eli didn't say anything, just waited until Adrian joined him in the lift and he pressed the button to take them to the Department of Mysteries. It was a secure there and his lab had everything he needed. If it came down to an issue of clearance, Pucey was an auror and these were dire circumstances. More importantly, it wasn't like Eli just left out sensitive information hanging about his lab. He certainly didn't trust his assistants not to muck up the hard work he did put in.
When the lift dinged and the doors opened on the ninth level, Eli exchanged a look with the man at the desk daring him to say something. It was actually the standard sort of greeting between the two of them. Eli glanced over his shoulder at Adrian and their test subject. "You start preparing that thing for transport while I get you cleared to come through." It was almost a question, except that he wasn't really giving Adrian the option to back out.
Leaving Adrian to arrange transport of the angry man fighting against his binds, he went over to explain quite plainly of the incident happening upstairs and how Auror Adrian Pucey was assisting him so that they could figure out just what was going on and properly neutralize the threat.