[5] Initially focusing on threats from far left groups such as the Japanese Red Army during the days of the Cold War, it began to conduct intelligence work on the Aum Shinrikyo after the Sarin gas attack on the Tokyo subway in 1995,[6] with criticism that the PSIA did not monitor the group, especially with their attempt to acquire and stockpile biological weapons on Japanese soil.

[10] The PSIA had cooperated with the Tokyo Metropolitan Police Department Public Security Bureau in investigating Aum Shinrikyo for a number of years.

"[11] The PSIA had investigated Aum Shinrikyo when it was revealed that the group had established software firms that could pose security risks to Japan.

[21] In January 2017, Okinawa press reported that the PSIA has conducted investigation into pro-Okinawan independence and anti-USFJ bases activist groups for potential links to China.

[24] On April 21, 2023, Hideji Suzuki, the former director of a Japan-China youth exchange association, suggested that the PSIA has a pro-Chinese mole that was behind his arrest in China for allegations of spying.

In the 2000s, the PSIA was reported to have conducted undercover operations at the Chinese-North Korean border by distributing flyers to locals in obtaining information regarding Japanese nationals abducted by North Korea.

[26] In 2003, it was reported that the PSIA had a mole inside Aum Shinrikyo by the name of Kazumi Kitagawa, who joined the cult after the sarin gas attack in the Tokyo Metro; she later tried to seek asylum in North Korea.

[6] In October 2018, Chen Wenqiang, head of the Chinese Ministry of State Security, visited the PSIA in order to collaborate on antiterrorism activities prior to the 2020 Tokyo Olympics.

[28] The PSIA has faced criticism in the past for being ineffective, in part because it has little ability to act without approval from the PSEC, an ad hoc body that meets only when required.