Shoigu was speaking at a meeting of the Shanghai Co-operation Organisation (SCO), a security grouping that includes Russia, India, China, Iran, Pakistan, Kazakhstan, Uzbekistan, Kyrgyzstan and Tajikistan.
Shoigu accused the US-led Quad and AUKUS blocs of trying to reshape the security structure in the Pacific to suit themselves and said increasing pressure was being exerted on China over Taiwan.
The Quad is a diplomatic partnership between Australia, India, Japan, and the US committed to supporting an open, stable and prosperous Indo-Pacific.
AUKUS - a trilateral security partnership between Australia, the UK and US - will see Australia kitted out with nuclear-powered submarines.
"I believe that everyone present shares the opinion that the deployment of military infrastructure in the region by the United States and its allies is unacceptable," Shoigu told the SCO meeting on Friday.
"Such intentions must be regarded as a direct threat to stability in the SCO space."
SCO member states should expand the scope and geography of their military exercises, he told the meeting in the Kazakh capital Astana.
His speech highlighted Russia's intention to strengthen military ties with partners in Asia and resist any erosion of its influence there despite the intense demands on its army of the war it has been fighting for more than two years in Ukraine.
At home, Shoigu's position is under greater-than-usual scrutiny after the arrest of one of his deputies this week in a bribery scandal - a development that threatens to weaken him politically.
Shoigu said the main threat in Central Asia came from "radical terrorist groups located in Afghanistan".
He said the US was working to restore influence in the region that it lost after the withdrawal of its troops from Afghanistan in 2021.
Islamic State militants claimed responsibility for killing more than 140 people at a concert hall near Moscow in April, and the US said it was the group's Afghan network that planned the attack.
Shoigu repeated Russia's assertion that Ukraine was behind it, an allegation that Kyiv has denied and Washington says is nonsense.
In Ukraine, Shoigu said foreign advisers were helping Kyiv prepare acts of sabotage on Russian territory, and that Ukraine was using Western weapons to attack Russian civilian infrastructure.
He did not provide evidence to back up his assertions.
