They've never stated it, although they have stated that they wouldn't state it.
IIRC there was a long thread awhile go that tried to quantify it. I think the best guess was 1% or less. I've got the full Mk XII space and ground set for my Fed main. I've been working on a Klingon alt. I've done nothing but elites on my klingon toon. It's taken me 100 runs or more to get a piece of proto tech. On my Fed Main it took around 150 Cure runs to get the gun tech.
So my best guess is the drop rate is between .5% and 1%, ie it will take between 100-200 runs of each STF to get all 6 pieces.
They need to make the drops a universal tech (Uncommon, Rare, or Prototype) that can be used to requisition a deflector, shield, or engine item of the tier appropriate for the drop item's rarity (Uncommon = Mk X, Rare = Mk XI, Prototype = Mk XII).
Having them unique like this is really annoying; I keep getting proto shield drops on ISE repeatedly when I run them all for EDC's/Dilithium, yet I can't get CSE to drop my proto engine tech to save my life.