When the royal authority moved against Pizarro in 1546, Carvajal, unable to quit the country due to the embargo on shipping, took command again in the field as Pizarro's lieutenant, or "Maestro de Campo" of Nueva Castilla's armies. In the campaign of 1546 Carvajal violently put down the royalist forces in the south of the colony, marching and countermarching from Quito to San Miguel, from Lima to Guamanga and back to Lima, from Lucanas to Cuzco, from Collao to Arequipa and from Arequipa to Charcas.