I think there's a problem with the way they teach English in Japan.
日本の英語教育のやり方に問題があると思う - I think there's a problem with the way they teach English in Japan もしくは I think there's a problem in the way English is taught in Japan になると思います。
I think the problem with the English education system in Japan lies in the way English is taught も大丈夫だと思います。
例文 -
I think the problem with the English education system in Japan lies in the way English is taught. There’s too much emphasis on test taking and rote memorization and not enough emphasis on actually speaking.
rote memorization – 丸暗記
test taking - 受験
イギリス 
