Moscow police rounded up and arrested more than 1,000 migrant workers at a vegetable warehouse on Monday, the day after Russian rioters staged the most violent nationalist unrest in the capital in three years.

Riot police battled and arrested hundreds of Russian nationalists on Sunday night after they overturned cars and raided a warehouse used by migrants in search of the man they blamed for the murder of an ethnic Russian.

Police on Monday responded by arresting more than 1,200 migrant workers in what was called a "pre-emptive raid" on the warehouse where the rioters believed the killer worked.

There were another 80 arrests of migrants at a warehouse in northern Moscow, while the Moscow mayor Sergei Sobyanin has ordered checks on other market places.

Sunday night's rioting in the southern Biryulyovo residential district of Moscow erupted after hundreds of Russians gathered at the spot where Egor Shcherbakov, 25, was stabbed and killed in front of his girlfriend on 10 October.

The following day a photograph of the alleged murder suspect, believed to be from the Caucasus region, was circulating on nationalist websites.

Nationalists said they were protesting that the killer, who has still not been publicly identified or found, was enjoying impunity.

Angry mobs overturned cars, smashed shopping centre windows and vandalised fruit stands before storming the warehouse searching for the alleged killer. Masked nationalists hurled bottles at police, who fought back with batons. The mobs chanted "Russia for Russians".

Six police officers were wounded; two were taken to hospital. About 380 nationalists were arrested on Sunday night, with all but two released from custody on Monday. . Seventy are to be fined.

Approximately 40 local residents from Biryulyovo staged a street protest on Monday evening, Interfax news agency reported. One of them carried a banner addressed to the authorities: "Admit the problem – start acting!"

The head of the Federation of Migrants warned migrants about the potential for random attacks by nationalists across the city. The violence has sent a chill through migrant communities, many of whom fear the police could carry out far-reaching checks on migrants in order to pacify nationalist outcry.

According to official statistics there are two million illegal migrants in Russia, although the real figure is believed to be much higher. Illegal migration represents a lucrative shadow economy built on corruption, bribes and false documents.

Residents from the former Soviet Union do not require visas to work in Russia and many, in particular from Central Asia, travel to Russia to escape high unemployment at home. "They don't understand that when they catch someone and deport them, they're deciding his fate. He can't return here for five years and there is no work over there," said Azamat, 36, a taxi driver from Uzbekistan working in Moscow for eight years.Police carried out a crackdown on illegal immigrants at market places in Moscow in the summer after a police officer was beaten at Matveev marketplace at the end of July. Police detained hundreds of migrants – many from Vietnam – in tent camps before deporting them.

Several police officers were subsequently jailed for taking bribes in return for protecting the migrants without necessary documents from the law.

Sunday's violence was the most serious nationalist unrest in the capital since December 2010, when the murder of a Russian football fan by a man from the North Caucasus ignited ultranationalist rioting at the foot of the Kremlin walls.

On Monday night the opposition leader and anti-corruption campaigner, Alexei Navalny, posted a petition on his blogging page in favour of introducing a visa regime for nationals from Central Asia and the South Caucasus. He wrote that 84% support the measure.