The media coverage of Mori's term as prime minister was dominated by his gaffes and undiplomatic comments, which led to him becoming unpopular in opinion polls.

After resigning as prime minister, Mori remained a member of the House of Representatives until announcing in July 2012 that he would not stand in the 2012 general election.

He remained an important player in Russo-Japanese relations following his resignation as prime minister due to his close personal relationship with Vladimir Putin.

[10] In the midst of a battle with Liberal Party leader Ichirō Ozawa, Prime Minister Keizō Obuchi suffered a stroke and cerebral hemorrhage on 2 April 2000 and was unable to continue in office.

[22] Hiromu Nonaka, the secretary general of the party, quashed the potential revolt by threatening to expel any LDP politicians who voted for the measure.

Although he denied the reports, they contributed to a massive drop in Japanese stock market prices early that week.

[30] Mori remained an important player in Russo-Japanese relations following his resignation as prime minister due to his close personal relationship with Vladimir Putin.

[32] Mori has a personal connection to Russia, as his father Shigeki Mori developed a relationship with the Siberian town of Shelekhov during his time as mayor of the city of Neagari, and developed a bilateral dialogue to improve the gravesites of Soviet soldiers in Japan and Japanese soldiers in Siberia; he was so close to Russia that Japanese authorities monitored him closely as a potential communist sympathizer.

It had been hoped his clout would help secure the 2011 Rugby Union World Cup for Japan, but instead the event was awarded to New Zealand in late November 2005.

[36] Another controversy occurred in 2021 when Mori, who at this time was president of the organization responsible for the upcoming Olympic Games, said that women talk too much in meetings.

[...] You have to regulate speaking time to some extent [...] Or else we’ll never be able to finish”[37] He apologized for his statements and initially stated he would not resign as head of the organizing committee,[38] but on February 11 announced his intention to step down from the post.

[39] In his resignation speech the following day, Mori said that he did not intend to demean women, and blamed the media for fueling public anger.

He stressed the importance that the Olympics be held in July, adding that the committee's efforts would be wasted if he were to cause trouble by remaining in his post.

[8] Seiko Hashimoto, an Olympic bronze medalist in women's speed skating and a seven-time Olympian, was named as Mori's replacement.

[40] As the former head of the Seiwa Seisaku Kenkyūkai, which was the main faction involved in the 2023–2024 Japanese slush fund scandal, Mori has come into question for his role in the kickback scheme.