Once considered sacred, the deer are now classified as a national treasure, so are protected by law.
訳すと「かつては神聖とみなされ、現在では鹿は国宝と分類されるので、法律によって保護されている。」です。Once considered sacredの部分は分詞構文になってます。この文も比較的平易ですね。では次の文へ。
Last year, the authorities said the deer were causing about 6bn yen ($54m; £41m) in damage to regional agriculture annually, so they would start taking action.
"Nara has a long history of people living side by side with deer in harmony. We want to continue efforts to coexist in peace while preventing damage to crops." one local government official told the Asahi Shinbun.