The picture above shows Aum Shinrikyo members outside during the raid.
Despite the horror that persists over the Aum's subway attack and other crimes, some experts had warned against the execution of Asahara and his acolytes.
He "lured young people, who felt a sense of emptiness in Japanese society", she said.
The attack in 1995 woke up a relatively safe country to the risk of urban terrorism. It was the worst terrorist attack to take place on Japanese soil.
The cult also carried out other crimes that together with the subway attack killed 27 people in total.
Though concerns about the Aum had already been raised, the attack prompted a massive crackdown on the cult's headquarters and the arrest of Asahara and other group members.
In a February 2004 ruling, the Tokyo District Court found Asahara guilty of all 13 charges and sentenced him to death, saying, "We can not help saying that the motivation and goal of the crimes were too outrageous and ridiculous, as he tried to control Japan in the name of salvation".
In 1995 it carried out a Sarin chemical attack that killed 13 people and injured thousands more.
Matsumoto insisted he did not instruct his followers to carry out the attacks.
The cult went underground after the 1995 attack, but did not disappear, eventually renaming itself Aleph or Hikari no Wa.
Japanese police tightened security Friday after the executions of the founder and six former senior members of the AUM Shinrikyo cult earlier in the day fanned fears about potential retaliation by followers. The initial death sentence in 2004 became final after his defense team could not file an appeal citing his mental state.
Japan forgoes executing death row inmates if an accomplice is still on trial. However, ultimately, the death penalty was given to Shoko Asahara and others high in the chain of this organization.
Aum Shinrikyo's killings began in November 1989, when lawyer Tsutsumi Sakamoto - who was working on a class action case against the cult - was brutally murdered along with his wife and child.
"The fear, pain and sorrow of the victims, survivors and their families - because of the heinous cult crimes - must have been so severe, and that is beyond my imagination", Justice Minister Yoko Kamikawa told a news conference.
The legal proceedings had been dragged out, but recent Japanese media reports said the executions were expected. The followers of the three groups total about 1,650 in Japan and about 460 in Russian Federation, while the groups hold more than 1 billion yen ($9 million) in assets, according to the agency.