Turkey's foreign ministry has summoned the Russian ambassador in Ankara to complain about protests against Turkish missions and businesses in Russia.
A ministry statement said that Turkish offices had come under what it called physical attacks disguised as protests, adding that Turkey had warned Russian authorities to urgently increase protection for the embassy and other Turkish interests.
Protesters in Moscow hurled eggs and stones at the Turkish Embassy on Wednesday, breaking windows in the compound.
Police cleared the area and made some arrests shortly after the protest began.
Meanwhile Russia plans to retaliate against Turkey following the downing of a warplane by imposing sanctions, cutting economic ties and scrapping major investment projects.
Since the plane was shot down in disputed circumstances on the Syria-Turkey border on Tuesday, Russia has already restricted tourism, left Turkish trucks stranded at the border and announced the confiscation of large quantities of Turkish food imports.
On Thursday, Russian prime minister Dmitry Medvedev ordered his government to also draft sanctions against Turkey within the next two days in response to the downing of the Su-24, which he described as an "act of aggression against our country".
The sanctions will include "restrictions and bans on Turkish economic structures operating in Russian territory, restrictions and bans on deliveries of products, including foodstuffs", as well as on labour and services.
Overall, the nosedive in relations threatens billions of dollars of international trade, as well as further complicating the Syrian conflict.
Russia is the largest destination for Turkey's exports, and the two countries are bound by plans for a new gas pipeline and strong trade in food and tourism.
Turkish president Recep Tayyip Erdogan met his Russian counterpart Vladimir Putin only two months ago and predicted a tripling of bilateral trade to 100 billion US dollars (£66 billion) in the next eight years.
The move came after Turkey released audio recordings of what it says are the Turkish military's repeated warnings to the pilot of the Russian plane before it was shot down.
The recordings indicate the plane was warned several times that it was approaching Turkey's airspace, and asked to change course.
The series of 10 audio clips were released by the Turkish prime minister's office and sourced to the Turkish Armed Forces.
In the recordings, a voice is heard saying in broken English: "This is Turkish Air Force speaking on guard. You are approaching Turkish airspace. Change your heading south immediately."
Most of the audio is garbled and barely comprehensible but the tone of the voice gets more agitated as the warnings appear to go unnoticed.
The audio that was released only involved Turkish warnings, no replies by a Russian pilot.
It was not clear whether Russian replies were received but not released by the Turkish government, or whether the Russian pilots never replied to - or never heard - the warnings.
One of the Russian pilots was killed by militants in Syria after ejecting from the plane, while his crewmate was rescued by Syrian army commandos. A Russian marine was also killed by the militants during the rescue mission.
Earlier, Mr Putin complained that he has received neither an apology from Turkey nor an offer "to make up for the damages" following the incident.
He also said Turkey has not given any assurances that "the culprits of this crime" will be punished.
Speaking at the Kremlin, Mr Putin said he regretted the fact that relations between Turkey and Russia have been driven into a stalemate.
However, Mr Erdogan later hit back at Russia, accusing it of using its fight against Islamic State in Syria as a pretext to target opposition groups in a bid to strengthen Syrian president Bashar Assad.
Without naming Russia openly, Mr Erdogan also challenged the country to prove its accusation that Turkey is buying oil and gas from IS, and called the claims "shameful".
He said Turkey was the country leading the most serious fight against IS, saying it had detained thousands of militants over the past few years.
Mr Erdogan added that Turkey had not specifically targeted Russia when it shot down the plane, saying it was "an automatic response" in line with its rules of engagement.
He said: "Faced with the same violation today, Turkey would give the same response."