"I am convinced that our meeting is going to contribute toward reinforcing friendly relations between Russian and Iranian armed forces," said Shoigu in a statement.
Iran's Hossein Dehghan and Shoigu spoke about "the necessary measures for the progressive development" of their military cooperation, based on the accord signed in January between Tehran and Moscow, the statement said.
The two countries are also "ready to coordinate their approaches on a large number of global and regional issues", Shoigu added, speaking in the "context of the growing crisis in the Middle East.
The Russian defence chief did not speak specifically about Syria, where Russia on September 30 sent in its warplanes to lauch air strikes at the request of Syrian President Bashir al-Assad, who is also supported by Iran.
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"Our countries face the same challenges and threats in the Middle East region and it is only together that we will be able to fight them," Shoigu said.
Iran and Russia, long-time allies of Syria, have also reinforced their military and nuclear cooperation since the signing in July of an historic accord between Tehran and the world powers on the Iranian nuclear programme.
Russia has authorised the delivery of S-300 anti-aircraft batteries to iran, despite the strong oppostion of the Western powers.
And November 23, Moscow lifted a ban on the sale and delivery of technological materiel tied to the nuclear industry after a meeting between Russian President Vladimir Putin and Iran's leader Hassan Rouhani.
Iran's defence chief who arrived on Monday in Moscow also met with Putin and Deputy Prime Minister Dmitri Rogozin.