すみません、この料理からキノコを抜いてもらえますか？ — Excuse me, could you remove mushrooms from this dish? (Restaurant · Dining, Formal — to staff, JLPT N3)

Gesture & etiquette

Point to the menu item and then gesture a 'removing' motion.

While requests for omission are often accommodated, some dishes are pre-made or contain ingredients that cannot be easily removed. Be prepared for a 'no'. Clearly state if it's an allergy.