In a nation where 91% of the population was officially Catholic, over 99% voted in favor of joining Austria with Nazi Germany due in part to official church support.
One month after the Austrian Anschluss of March 12, 1938, Austrians went to the polls in a national plebiscite to ratify the joining of Austria with the Nazi Reich. Over 99% of Austrians voted “yes,” having been swayed by unending propaganda in the presses, pressure from the Austrian Nazis, and in some cases, the blessings of the hierarchy of the Catholic Church, notably Theodor Cardinal Innitzer of Vienna. The motivation of the Catholic hierarchy is still debated today, but several apparent reasons are well documented.
Cardinal Innitzer and the Plebiscite Vote to Join Austria with Nazi Germany
Cardinal Innitzer was both a German nationalist and an opponent of Marxism. In this, the leader of the Austrian Catholics embodied the two greatest arguments for union with the German Reich, shared by other German bishops and much of the population. The April 10th, 1938 ballot asked the Austrian people a simple question: “Do you pledge yourself to our Fuehrer Adolf Hitler and therewith to the reunification of Austria with the German Reich carried out on March 13th?” 
The statement appealed to the nationalist sentiment felt by many Austrians. One Catholic newspaper, the Passauer Bistumsblatt, stated that “it corresponds to the natural order set by God if…men speaking the same language and of common blood and ancestry are joined in a great Reich of the Germans.”  Although many Catholic newspapers by this time supported Hitler’s Reich, even over objections by some bishops, the Bishop of Passau enthusiastically supported “the Great German Fatherland.”
Catholic Fears of Communism
Cardinal Innitzer’s other worries concerned Marxism. The Catholic Church had long feared this movement and historians note that many church leaders, if given the choice, preferred National Socialism to Communism. According to Evan Bukey, the “Catholic hierarchy concluded that only the restoration of an authoritarian order could reverse the secular trends of the age…”  National Socialism’s fierce opposition to Communism made it easier to accept this new authoritarianism as long as the church was permitted to keep its prerogatives.
The Catholic Church Betrayed by Hitler and the Nazis
Following the plebiscite vote in April, the church continued to negotiate with the Nazis although the new regime had already closed parish schools, confiscated church lands, and silenced Catholic opposition. The attack on Cardinal Innitzer’s Episcopal residence following his leadership in what the Nazis perceived as an anti-government demonstration at St. Stephen’s Square, was one of the final acts demonstrating Hitler’s ultimate desires in emasculating the Austrian Catholic Church.
In retrospect, Innitzer’s naïve belief that he could maintain the Concordat of 1933 and seriously negotiate with the Nazis undermined the ability of the church to speak with one voice. Playing into the hands of duplicitous Nazi negotiators, the church urged a “yes” voted at the plebiscite, realizing afterward the folly of their actions. For its part, the Vatican severely critized Innitzer and other bishops for not taking a stronger stand against National Socialism and the protection church prerogatives such as marriage and education.
-  quoted in The Catholic Church and Nazi Germany by Guenter Lewy, (New York: McGraw-Hill Book Company, 1964) p. 217.
-  IBID p. 216.
-  Evan Burr Bukey, Hitler’s Austria: Popular Sentiment in the Nazi Era 1838-1945 (University of North Carolina Press, 2000) p. 93.