How long does it take for the navy to send an active secret clearance to the coast guard?

It was many moons ago, but when I was in it took about a week to get full clearance. Command may have expedited it, as I was replacing an ET-1 who had been busted twice for incompetence, and transferred off. As LPO for Electronics I had to have access to CIC, Radio, Crypto and IFF, and I had to have it like yesterday since much of the equipment was casrepped.

Just curious, but why are you hopping over to the Puddle Jumpers?

There is no real time associated with this process. In fact the CG should have direct access to verify your clearance. I would ask your CG POC to clarify. What it may be is that the CG is validating and determining reciprocity or not. The transfer of the clearance is what takes the time.