Pyongyang reportedly made preparations for a missile launch last month.
It had threatened attacks on specific targets on South Korea, Japan and US bases in the region.
The threats followed tough new UN sanctions imposed on North Korea in March after its third nuclear test.
Pyongyang has also been angered by wide-ranging annual US-South Korea military drills, which were completed a week ago.
The US flew nuclear-capable B2 and B52 bombers over the South as part of the drill, and deployed warships with missile defence systems to the region.
A new series of joint anti-submarine drills began on Sunday and will last until Friday, South Korea’s Yonhap news agency reports.
The Musudan missiles had been ready to launch at any moment but North Korea had now “moved them”, a unnamed US defence official told AFP news agency.
The move is the most tangible sign yet that North Korea has stepped back from its threats to launch missiles, the BBC’s Jane Little in Washington reports.
But a senior US official from the National Security Council warned that, given the North’s unpredictable behaviour, it was “premature to celebrate it as good news”,
Meanwhile Pentagon spokesman George Little, who declined to comment directly on the missiles’ reported removal, told reporters “what we have seen recently is a provocation pause”.
“And we think that’s obviously beneficial to efforts to ensure we have peace and stability on the Korean peninsula.”
North Korea unveiled medium-range Musudan missiles during a military parade in 2010 but had not yet tested them.
Last month, South Korea raised its alert level to “vital threat” amid indications that Pyongyang was preparing for a missile launch.
At least one ballistic missile with an estimated 3,000km (2,000-mile) range had been fuelled and ready for launch, according to US and South Korean sources.
A test launch would be a violation of UN Security Council Resolution 1718, passed in 2006, which states the North “must not conduct any further nuclear test or launch of a ballistic missile”.
Since the new UN sanctions were imposed, Pyongyang has threatened to use nuclear weapons and said it would restart a nuclear reactor.
In addition, it withdrew some 53,000 workers in April from the Kaesong factory zone on the border with South Korea.
The industrial complex, which was launched in 2003, employed people from both countries and was seen as one of the last remaining symbols of inter-Korean co-operation.
The final South Korean workers left the factory last Friday.
The North also shut down an emergency military hotline between Seoul and Pyongyang.