Wakabayashi became the third Minister of Agriculture, Forestry and Fisheries appointed in Shinzō Abe's first cabinet after Toshikatsu Matsuoka killed himself as a result of financial scandal and Matsuoka's successor Norihiko Akagi resigned due to other financial scandals.

He was appointed to the same position again in Abe's first reshuffled cabinet after Takehiko Endo's resignation.

After Abe's resignation, he worked under Yasuo Fukuda, who appointed Seiichi Ota his successor.

After the LDP were defeated in the 2009 election, it was unclear who would be their candidate in the diet nomination for prime minister, since Taro Aso had already announced his resignation as party president and no successor had been chosen.

The party ultimately decided to nominate Wakabayashi, who was then chairman of the general assembly of LDP diet members, for Prime Minister, though he had no hope of being elected.