The move is just the latest in a string of Russian provocations in the early days of the Trump administration, which has called for warmer relations with the Kremlin.
The traditional US adversary has also positioned a spy ship off the coast of Delaware and carried out flights near a US Navy warship, concerning American officials. The administration has not officially drawn any links between the three events.
The ground-launched cruise missile seems to run counter to the 1987 Intermediate-Range Nuclear Forces (INF) Treaty, the senior military official said. The New York Times first reported is deployment.
While declining to speak on intelligence matters, a spokesman for the US State Department did draw attention to Russian violations of the treaty.
"The Russian Federation remains in violation of its INF Treaty obligations not to possess, produce or flight-test a ground-launched cruise missile with a range capability of 500 to 5,500 kilometers, or to possess or produce launchers of such missiles," acting spokesman Mark Toner said in a statement issued Tuesday.
Russia is believed to have tested one such missile in 2014.
Trump has in the past expressed interest in arms reduction talks with the Kremlin and indicated he would seek a new opening with Moscow.
White House press secretary Sean Spicer, however, said Tuesday that, "The president has been incredibly tough on Russia."
Spicer pointed to UN Ambassador Nikki Haley's recent remarks on the Russia's actions in east Ukraine and occupation of Crimea, adding that Trump "expects the Russian government to deescalate violence in the Ukraine and return Crimea."
"At the same time he fully expects to and wants to be able to get along with Russia unlike previous administrations," he added.
In a Tuesday evening tweet, the Russian embassy in Washington said Russia "will continue to patiently explain to the new US administration why Crimea is Russia."
Trump himself, though, repeatedly praised Putin on the campaign trail as well as since being elected, while offering few if any criticisms.
Asked about sanctions against Russia, newly minted Treasury Secretary Steven Mnuchin said Tuesday that sanctions were an important tool but would not specify any intensions towards Russia.
"Our current sanctions programs are in place, and I would say sanctions are an important tool that we will continue to look at for various different countries. But it's a very important program within the Treasury Department," Mnuchin said.
In contrast, Sen. Tom Cotton, an Arkansas Republican, called for a strong response to the cruise missile.
"If the last administration showed us anything, it's that ignoring these kinds of provocations simply means they will proliferate," he said in a statement. "I've said before we need to set firm boundaries for Russia's behavior -- and enforce them to the hilt. I take this news as evidence that the US should build up its nuclear forces in Europe."