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The incident happened after Turkey last month downed a Russian bomber at the Syrian border, leading to the biggest crisis in ties between the two countries since the end of the Cold War.
After the downing of the warplane, which led to the deaths of a pilot and another serviceman who attempted to rescue him, Russia introduced economic sanctions against Turkey and beefed up its firepower at its airbase in Syria.
At 0603 GMT Sunday the Russian warship, which was at anchor, spotted a Turkish fishing boat some 1,000 metres (yards) away, which had been approaching it from the right, the ministry said.
"Despite numerous attempts by the Smetlivy, the crew of the Turkish seiner would not engage in radio contact and did not respond to special visual signals," the ministry added.
Moscow said the crew had to fire small arms in the direction of the boat at "a guaranteed survivability distance" when the two vessels were about 600 metres apart "to prevent the collision of the ships."
"Immediately after that the Turkish vessel drastically changed course and continued its movement past the Smetlivy at the distance of 540 metres without engaging in contact with the Russian crew," the ministry said.
Turkish Foreign Mevlut Cavusoglu, who was in Rome, said that Ankara was investigating the incident and would make a formal statement when it had heard the Turkish vessel's side.
"We are not in favour of tensions. We have always been in favour of overcoming tensions through dialogue rather than conflict," he added, quoted by Dogan news agency.
Speaking to Dogan, however, the Turkish boat's captain denied that it had his boat been fired at, saying: "It's a lie. There is no such thing."
"We passed within a mile of a warship which was at anchor. We didn't even know that it was a Russian ship, we thought it was a NATO ship. We didn't realise we had been fired at," Muzaffer Gecici said.
- 'Happy coincidence' -
Deputy defence minister Anatoly Antonov summoned a Turkish military attache, Ahmet Hakam Gunes, after the incident.
He warned him against the "negative consequences of any thoughtless action by Ankara against a Russian military contingent" deployed in Syria, the ministry said.
He also said Russia was "gravely concerned over the Turkish side's provocative acts regarding Russian destroyer Smetlivy."
"It is merely thanks to a happy coincidence that we were able to avoid a tragedy," the statement added.
President Vladimir Putin on Friday delivered a thinly veiled warning to Ankara and told his forces in Syria to take tough action against any threats.
"I would like to warn those who would once again try to organise some sort of provocations against our servicemen," Putin said.
Cavusoglu said on Friday that Ankara's patience with Moscow after the downing of the warplane was "not unlimited".
Earlier Sunday, the Turkish military banned personnel from taking holidays in Russia, branding it a "precautionary measure after the Russian warplane, which violated (Turkey's) borders, was downed in accordance with the rules of engagement," Turkey's state-run Anatolia news agency said.
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After the downing of the warplane, which led to the deaths of a pilot and another serviceman who attempted to rescue him, Russia introduced economic sanctions against Turkey and beefed up its firepower at its airbase in Syria.
At 0603 GMT Sunday the Russian warship, which was at anchor, spotted a Turkish fishing boat some 1,000 metres (yards) away, which had been approaching it from the right, the ministry said.
"Despite numerous attempts by the Smetlivy, the crew of the Turkish seiner would not engage in radio contact and did not respond to special visual signals," the ministry added.
Moscow said the crew had to fire small arms in the direction of the boat at "a guaranteed survivability distance" when the two vessels were about 600 metres apart "to prevent the collision of the ships."
"Immediately after that the Turkish vessel drastically changed course and continued its movement past the Smetlivy at the distance of 540 metres without engaging in contact with the Russian crew," the ministry said.
Turkish Foreign Mevlut Cavusoglu, who was in Rome, said that Ankara was investigating the incident and would make a formal statement when it had heard the Turkish vessel's side.
"We are not in favour of tensions. We have always been in favour of overcoming tensions through dialogue rather than conflict," he added, quoted by Dogan news agency.
Speaking to Dogan, however, the Turkish boat's captain denied that it had his boat been fired at, saying: "It's a lie. There is no such thing."
"We passed within a mile of a warship which was at anchor. We didn't even know that it was a Russian ship, we thought it was a NATO ship. We didn't realise we had been fired at," Muzaffer Gecici said.
- 'Happy coincidence' -
Deputy defence minister Anatoly Antonov summoned a Turkish military attache, Ahmet Hakam Gunes, after the incident.
He warned him against the "negative consequences of any thoughtless action by Ankara against a Russian military contingent" deployed in Syria, the ministry said.
He also said Russia was "gravely concerned over the Turkish side's provocative acts regarding Russian destroyer Smetlivy."
"It is merely thanks to a happy coincidence that we were able to avoid a tragedy," the statement added.
President Vladimir Putin on Friday delivered a thinly veiled warning to Ankara and told his forces in Syria to take tough action against any threats.
"I would like to warn those who would once again try to organise some sort of provocations against our servicemen," Putin said.
Cavusoglu said on Friday that Ankara's patience with Moscow after the downing of the warplane was "not unlimited".
Earlier Sunday, the Turkish military banned personnel from taking holidays in Russia, branding it a "precautionary measure after the Russian warplane, which violated (Turkey's) borders, was downed in accordance with the rules of engagement," Turkey's state-run Anatolia news agency said.
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