In the Operational Procedures subject, a good rule for answering questions is that:

• The operator establishes
• The competent authority approves

Using this simple rule: 'who approves the method for establishing minimum flight altitudes?' Answer: the competent authority.

EASA AIR OPS
Regulation (EU) No 965/2012
CAT.OP.MPA.145 Establishment of minimum flight altitudes

(a) The operator shall establish for all route segments to be flown:

(1) minimum flight altitudes that provide the required terrain clearance, taking into account the requirements of Subpart C; and
(2) a method for the flight crew to determine those altitudes.

(b) The method for establishing minimum flight altitudes shall be approved by the competent authority.

(c) Where the minimum flight altitudes established by the operator and a State overflown differ, the higher values shall apply.