Due to its time-consuming and labor-intensive recipe and the dwindling number of funa and nigoro buna, that are most suitable for making funa-zushi, caused by various factors including the decreased reed fields, deteriorating water quality, destruction of breeding grounds by concrete embankment and fish of foreign origin in the lake, the price of these fish species has steeply risen to several thousands of yen each in recent years and, in some cases, funa-zushi is made with gengoro buna (Carassius cuvieri) and gin buna (Carassius langsdorfii) in substitution for funa and nigoro buna.
近年、手間と時間のかかる製法であることや、材料として最も適する種類のフナであるニゴロブナが湖岸のヨシ原減少や水質の悪化、湖岸のコンクリート護岸化にともなう産卵床破壊、外来魚などにより減少していることで価格が1尾数千円と高騰し、ゲンゴロウブナやギンブナを代用したものも作られている。