In mid-1948, Kawilarang was included in a contingent of government and military officials to Bukittinggi in West Sumatra. The move was in anticipation of a second Dutch military aggression and to allow the formation of an Indonesian emergency government outside of Java. Kawilarang was assigned to lead the Seventh Sub-Territorial Command (or "Komando Sub-Teritorial VII") for Tapanuli and the southern region of East Sumatra. One of his tasks was to stop the infighting between factions of the army in the area. When the Indonesian government-in-exile was enacted because of Operation Kraai (the second Dutch military aggression against Indonesia), Kawilarang was also appointed as Deputy Military Governor of the same region in Sumatra with Ferdinand Lumbantobing appointed as Military Governor.