The 'Kreuzpflicht' law, or 'crucifix mandate' was decided by Minister-President Markus Söder from the Christian Social Union party and the Bavarian Cabinet.
He called it an "affirmation of our cultural and historical, as well as our spiritual values."
The Free State of Bavaria is predominantly Catholic and the move is being seen as an attempt to secure their traditional majority in elections in October.
The leader met the Pope this week, just before the rule came into force.
However, the rule has been opposed by bishops in the state.
According to the Guardian, the incoming bishop of Würzburg, Franz Jung said: "The crucifix is a genuine religious symbol and it should not be reduced to a folkloric object and regional custom.
The Süddeutsche Zeitung report that Cardinal Reinhard Marx, the head of the Catholic German Bishops' Conference, said: "If the cross is only seen as a cultural symbol, it has not been understood."
The archbishop of Munich and Freising said: "Then the cross would be expropriated in the name of the state."
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