In the mid-1940s and with official blessing of the military, Marco was appointed jefé of Navascués zone militia, deployed in anti-maquis operations. Initially his relation with the 1945-appointed civil governor was excellent; both toured Navarre and Marco contributed with his expert knowledge about people and places. However, he soon concluded that Junquera advanced a centralist vision aimed against traditional separate Navarrese establishments, and the two developed mutual hostility. In 1948 Marco travelled to Madrid to denounce Junquera and to prove that genuinely attached to Franco, the region might get skeptical when stripped of its fueros. In late 1948 he resigned his position of sub-jefé of Movimiento in Navarre as means of protest against governor's policy. Running on firmly anti-Junquera ticket in 1949 Marco was re-elected to his second successive term in Diputación; despite his dissent, in 1949 he was also re-appointed to the FET Consejo Nacional.