After Nazi Germany imposed the Protectorate of Bohemia and Moravia in March 1939, Klapálek joined a Czech military anti-Nazi resistance organization "Obrana národa" (Protection of the Nation) in České Budějovice. After the organization was destroyed in 1940 he fled the country and reached Mandatory Palestine, where he joined the 4th Czechoslovak Infantry Regiment, later reorganised as the Czechoslovak 11th Infantry Battalion (East), with Klapálek as its commander. The battalion fought in the Allied invasion of Syria and Lebanon in June and July 1941, and was then stationed on the Turkish border in August. From October to December 1941 the battalion fought in the defence of Tobruk under the command of the Polish Independent Carpathian Rifle Brigade.