The Munich Agreement ended the First Republic of Czechoslovakia. Its previous pro-democratic and anti-totalitarian policies gave way to calls for authoritarian government and closer cooperation with Nazi Germany. The political elite, connected with former PresidentEdvard Beneš, had to leave office and Chvalkovský became foreign minister. He tried to maintain the independence of the rump state by making concessions to neighbours, hoping to gain time for a more favorable outcome in the future. He grossly underestimated Hitler's desire to occupy Central Europe and the hunger for revenge from Poland and Hungary, who had been forced to make painful concessions to Czechoslovakia after World War I. He represented Czechoslovakia during the Vienna Arbitration. Due to insufficient preparation, Czechoslovakia had to concede significant parts of Slovak territory to Hungary. When Slovakia declared independence on 14 March 1939, Chvalkovský traveled with President Emil Hácha to Berlin, hoping that further concessions would preserve the independence of Czech lands.
With the establishment of the Protectorate, there was no official place for the Czech diplomatic service. As a last ruling, under German pressure, the Foreign Ministry ordered all Czechoslovak ambassadors to close their embassies and to transfer them to the Germans. Patriotic clerks hoped that the ambassadors, free from direct Nazi pressure, would disobey the order and keep the embassies for the future benefit of the government-in-exile. As a last resort, if the host government were hostile to them, they should transfer their embassy to the host government, rather than Germany. However, many ambassadors did not read between the lines and obeyed the order literally, as they usually did, causing significant damage to Czechoslovak interests. Given the sequence of events shaped by Chvalkovský, many countries, such as France, a signatory of the Munich Agreement, initially considered the fall of Czechoslovakia a result of internal forces, rather than German aggression. Chvalkovský thus caused considerable damage to Czechoslovakia during this critical period. After the Foreign Ministry was closed in 1939, Chvalkovský became an envoy of the Protectorate in Germany. He was killed on a highway outside Berlin during an Allied Air raid, strafed by a low-flying aircraft. The German High Command reported British strafing attacks near Berlin on that day.
