The Russian military said the Liman — a former research ship re-fitted as an intelligence vessel — had a hole ripped out of its hull in the early afternoon incident, according to France 24 agency.
The collision took place in fog outside the northwestern entrance to the Bosphorus Strait, one of the world’s biggest shipping thoroughfares that passes through Istanbul into the Sea of Marmara.
The Turkish coastguard said in a statement that the collision involved the Togo-flagged vessel Youzarsif H which was carrying a cargo of livestock.
It said that of 78 Russian personnel on board the ship, 63 were rescued by the Turkish coastguard and the other 15 by the Youzarsif H itself.
They were then transferred to a Turkish military ship, it said, without giving further details. “All the personnel were evacuated,” it said.
Turkish media said the Youzarsif suffered minor damage and went on its way after the incident.
The Russian defence ministry confirmed the ship had gone down and said the crew were safe and would be taken from a Turkish vessel back onto a Russian ship.
Turkish news agency Dogan said the area where the ships collided was shrouded in thick fog at the time, suggesting that the incident was accidental.
Turkish Prime Minister Binali Yildirim spoke to his Russian counterpart Dmitry Medvedev by phone over the incident, describing it as an accident and expressing his sadness, the state-run Anadolu news agency said.
It was not known where the Liman was sailing from or its destination.
The ship was built as a hydrography research vessel in 1970 but turned into a spy ship in 1989 and armed with an Igla missile launcher, according to public records.
Russian warships have travelled frequently through the Bosphorus Strait to and from the Syrian coast, where a navy presence has been deployed to bolster Russia’s air campaign in support of President Bashar al-Assad.
In February, military sources told Russian media that Liman would be observing NATO’s Sea Shield exercise in the Black Sea.
Cem Devrim Yaylali, an Istanbul-based Turkish naval expert and editor of the Bosphorus Naval News website, said the Liman had previously been to the Syrian coast but it was not clear where it was headed on this occasion.
“A collision is not something that happens very frequently,” he told AFP.
He said the incident was an embarrassment for the Russian authorities as the Liman was likely carrying sensitive surveillance equipment that Moscow would want returned.
“I imagine there will be a salvage effort to raise the ship before anyone else sees it,” he said.
“If the ship cannot be salvaged then Russia surely will try to take away the sensitive equipment from on board by divers.”
Relations between Russia and Turkey hit their worst state since the Cold War in November 2015 when Turkish war planes shot down a Russian jet over the Syrian border.
But there has since been a dramatic reconciliation, with Moscow and Ankara now engaged in a joint effort to bring peace to Syria despite standing on opposing sides of the conflict.
President Recep Tayyip Erdogan is due to hold his latest talks with Russian counterpart Vladimir Putin in Russia on May 3.
As a Black Sea littoral state, Russia is allowed to have its military ships pass through the Bosphorus under the 1936 Montreux Convention on the Straits.
The intense traffic of Russian vessels to and from Syria — known as the Syrian Express — has caused immense curiosity in Istanbul where the warships pass through the heart of the city in full view of ship-spotters.