For Japan's Trade and Industry Minister, Banri Kaieda, the three senior officials were responsible for mishandling the plant and the problems that followed the incident.
Those sacked are the head of the nuclear safety agency, Nobuaki Terasaka, the head of the agency for natural resources and energy, Tetsuhiro Hosono, and the deputy minister for the Economy, Trade and Industry, Kazuo Matsunaga.
Mr Kaieda, who played a key role in managing the Fukushima crisis, also said he plans to resign to take responsibility.
Recently, Prime Minister Naoto Kan has said the country must shift towards alternative energy sources.
Meanwhile, the government plans to introduce new nuclear safety regulations to ensure greater security and responsibility.