The Spanish government has been accused of further provocative behaviour over the contested British territory of Gibraltar after it allowed a Russian submarine to refuel at one of its ports just 19 miles from the Rock.

Security sources now fear that the state-of-the-art Novorossiysk, which passed through the English Channel last week, may now operate from a Russian naval base on the annexed Ukrainian peninsula of Crimea, The Independent can reveal.

Conservative backbenchers and defence experts have been quick to condemn the three-day visit by the Russian hunter-killer submarine to the port of Ceuta, a contested Spanish enclave on the Moroccan coast.

Ceuta is often described as Spain’s Gibraltar and is just 19 miles across the water from the British Overseas Territory, prompting a Conservative MP to label the visit a “clear provocation” by Spain designed to “intimidate the Gibraltarian people”.

Critics have said that while Spain appears reluctant to confront Russia, it’s taking an increasing firm line over Gibraltar where a Spanish customs boat allegedly fired on a Gibraltar-flagged pleasure boat last Saturday, the third such incident in as many weeks.

The rock of Gibraltar (Frans Lemmens / Getty Images)

Andrew Rosindell MP, vice chairman of the All Party Parliamentary Group on Gibraltar, said: “Spain has consistently ignored the borders of Gibraltar’s territorial waters, rammed their ships, and even fired shots at boats filled with tourists. And now, to cap it all off, they are allowing the navy of an unfriendly power to park their submarine less than 18 miles away.”

The Independent understands the Russian vessel, which departed from Ceuta on Friday, took on supplies fuel and water to complete its journey from a northern Russian port to the Black Sea, while its 56-strong crew was granted shore leave to enjoy the tax haven’s nightlife.

Novorossiysk is an upgraded version of the Cold War Kilo-class submarine, known to Nato as Project 677. It is one of the quietest diesel class boats in the world, prompting the nickname “Black Hole”. She is set to join the Russian Black Sea Fleet where she will be used for intelligence gathering, tracking Nato submarines and potentially deploying special forces.

Concerns about the visit to Cueta have also been raised by security analysts, who fear the refuelling stop illustrates Europe’s lack of resolve in confronting Russian aggression in eastern Ukraine.

Luke Coffey, a security expert with the Heritage Foundation told The Independent: “For the past 18 months Nato has been focused on confronting Russian aggression in Ukraine, but here we have a Nato member actively hosting an advanced Russian warship on its way to the Black Sea. It’s crazy, and it will raise eye-brows in Washington.”

The Russian military has said the vessel is en-route to the Russian naval base at Novorossiysk, the Black Sea port from which it takes its name. However security experts have warned it “far more likely” to be headed for a major Russian naval base at Sevastopol in the annexed Crimean peninsula.

“It looks terrible for the Spanish if it’s hosting a submarine that is headed for occupied territory,” added Mr Coffey. “There will be a huge outcry in Washington, especially given the hypocrisy of Spanish rules that mean a US or Nato vessel cannot dock in Spain if it originates from Gibraltar. It’s ridiculous, as Spain is essentially saying they would rather have a Russian ship in one of their ports than a Nato vessel visit Gibraltar.”

Confirming the visit, a Nato official insisted the alliance had “suspended all practical cooperation with Russia” and the visit was “arranged bilaterally between sovereign nations”. The Spanish government did not respond to a request for comment on Friday.

The visit is not in breach of EU sanctions and Peter Roberts, a senior research fellow for sea power, at the Royal United Services Institute, said it may actually have a benefit to Nato.