The incident involving the Russian frigate Admiral Grigorovich and a 12-metre-long sailing yacht called the Bright Future happened about 20 nautical miles south of the Isle of Wight, outside the UK's territorial waters.
There were no injuries and the yacht was not damaged.
"Following attempts to contact a British vessel in the Channel, the Grigorovich fired warning shots," an MoD spokesperson said.
"These were not aimed at the vessel and were an attempt to prevent a possible collision."
The warship had been drifting rather than being manoeuvred under power, it is understood.
Russian warships passing through the English Channel are routinely shadowed by the UK royal navy, with offshore patrol vessel HMS Mersey monitoring the Admiral Grigorovich about 11.40am - the time of the incident - on Tuesday.
A boat from HMS Tyne, another patrol vessel, was sent to the yacht to gather details and check on the safety of the crew.
The Russian defence ministry said the warship fired warning shots to divert the yacht that approached on a dangerous course in the Channel.
The yacht altered course and moved away after the frigate Admiral Grigorovich fired warning shots, following failed attempts to establish radio contact, the Russian government said.
On Sunday, UK commandos boarded and intercepted a sanctioned Russian "shadow fleet" oil tanker in the Channel, leading for the first time an operation to disrupt the oil revenue that helps fund Russia's war in Ukraine.
A UK spokesperson said Tuesday's event was not viewed as being linked to that operation and was being treated as an isolated incident.
The Russian defence ministry said on Telegram that the yacht had been on a "dangerous approach" and the warning shots were fired after attempting to draw the attention of the yacht's crew through signal flares and sound signals.
It said the Russian sailors had acted "in strict accordance" with international shipping regulations.
The Russian statement identified the vessel involved as the Bright Future – a 12-metre-long sailing yacht which was en route to Cherbourg, France.
Martin Kelly, head of advisory at crisis management firm EOS Risk Group, said people should "be careful" not to link the incident with the seizure of Russian tanker Smyrtos by the UK two days ago.
He told the Press Association: "Warships, it doesn't matter who you are or where you're from, are entitled to self-defence.
"If a ship, yacht, etc is approaching, the rules of force escalation will start with a VHF (very high frequency radio) warning, and if there is no response the next escalation is a more intense warning, and then up to warning shots, which is where we got to here."
with Reuters
