I've read that after the Mukden incident the government in Tokyo had no intention to invade all of Manchuria, and it was the local army command that chose to go forward with this. Why wasn't the Japanese government able to restrain it's army in this situation?
The army was able to intimidate the civilian government through a series of right-wing terrorism coming from within the military. The assassination of the prime minister Inukai Tsuyoshi is an example. The attempted Coup in 1936 was another.
By design from the Meiji constitution, the military services had a vast amount of power over the Japanese civilian government. The service ministers sat on every cabinet meeting and had the power to veto every act.
The discreditation and loss of legitimacy of the pseudo-liberal civilian government because of its inability to handle the great depression. The rise of the imperial way faction in the Kwantung army, which advocated fascistic ideology of a totalitarian state and colonial expansion as means of solving Japan's woes and therefore gave ideological justification for refusing to follow instructions from Tokyo.