The system is dual-purpose meaning it could also be used by the Japanese to launch attacks which if actioned would violate Japan’s constitutional ‘no war’ clause.
Following its defeat at the end of the Second World War, Japan signed a deal promising to convert its military into a defensive force.
Last month Japan formally decided it would expand its ballistic missile defence system with radar stations and interceptors made by the firm Aegis.
The move is said to be a response to a growing threat from North Korean rockets.
Russian foreign minister Sergei Lavrov, speaking at his annual news conference in Moscow, said he doubts claims that the US would not be involved in the operational control of the system.
Mr Lavrov added that its deployment would cast a shadow over Moscow’s ties with Tokyo.
It comes just two months after Russian President Vladimir Putin told his country’s biggest enterprises to be war-ready.
He told firms that they must show they can step up arms production and important services on short notice.
Mr Putin told military leaders and senior officials in November: “The economic ability to increase the production of defence products and services quickly is a vital element of military security.
“All strategic and simply large companies, regardless of the type of ownership, must be able to do this.”
Japan approved a record military budget last month, with defence outlays due to rise for a sixth year, increasing by 1.3 percent to 5.19 trillion yen (£34billion), with the biggest item 137 billion yen in reinforcing defences against North Korean ballistic missiles.
It comes as foreign ministers from around 20 nations plan to gather on Tuesday to discuss how to curb North Korea’s nuclear ambitions through diplomatic and financial pressure, but China, seen as a key player in any long-term solution, will be absent.
The Vancouver meeting, co-hosted by Canada and the United States, comes amid signs that tensions on the peninsula have eased, at least temporarily. North and South Korea held talks for the first time in two years last week and Pyongyang says it will send athletes across the border to the Pyeongchang Winter Olympics.
But the US and others say the international community must look at ways of expanding a broad range of sanctions aimed at North Korea’s nuclear program.
Brian Hook, the State Department’s director of policy planning, said: “There is growing evidence that our maximum pressure campaign is being felt in North Korea. They are feeling the strain.”
North Korean leader Kim Jong-un has shown no sign of willingness to give in to U.S. demands and negotiate away a weapons program he sees as vital to his survival.