Lawmaker Jerzy Montag of the opposition Greens party on Tuesday described Merkel's comments as "mistaken" and "not very helpful".
Rights campaigners said ranking faiths according to how persecuted they are is pointless.
Human Rights Watch noted that Muslims in Myanmar, members of Falun Gong in China and Jews in many countries worldwide also face persecution.
Merkel's comments came at a meeting of the German Protestant Church late Monday in which she emphasized Germany needed to protect Christian minorities as part of its foreign policy.
Merkel, the daughter of a pastor, also spoke out against strict separation of church and state and said Europe was built on Christian foundations.