The very good 'TSR2 with Hindsight' document linked earlier says this:
Ivan Yates of English Electric,. BAC and BAe, reported that he had had an absolute denial from Denis Healey himself, which he accepted,
that he had given the instruction to destroy all trace of TSR2. Given
the structural and organisation ‘shambles’ of the project, it was
conceivable that almost anyone within it might have given the order.
Logically, somebody evidently gave an order; it just wasn't specifically Healey.