On January 20, 1991 the Riga OMON attacked Latvia's Interior Ministry, killing six people during the January 1991 events in Latvia (following the republic's declaration of independence). Seven OMON members were subsequently found guilty by the Riga District Court and received suspended sentences. A series of hit and run attacks on border outposts of the newly-independent Republic of Lithuania during January-July 1991 resulting in several summary execution style deaths of the unarmed customs officers. Some sources say that the Soviet leader Mikhail Gorbachev had lost control of the unit. The Lithuanian government continues to demand that the persons suspected in these incidents be tried in Lithuania. Violent and often armed clashes occurred between the Georgian SSR's OMON and the opponents of the Georgian President Zviad Gamsakhurdia prior to the Georgian Civil War of 1991-1993.
The Moscow OMON and units brought in from the other cities took part in defending the public order during the political crisis in September-October 1993. Some sources report that OMON members behaved brutally in clashes with demonstrators, beating up people including members of the Supreme Soviet of Russia.

In August 1996 a group of 30 Chechen OMON members were reportedly captured and executed in Grozny, the Chechen capital during the battle for the city. In June 2007 OMON failed to protect gay rights activists including  European Parliament members from hate violence in Moscow, detaining the activists instead of the attackers. This is because the mayor of Moscow did not want the parade to take place. In November 2007 the brutal actions of OMON militsya against peaceful demonstrators and the arrests of opposition figures were harshly criticised by the European Union institutions and governments.

OMON is still active in the Second Chechen War. Almost every Russian city sends on a regular basis small units of police (often composed of OMON members) for tours of duty in Chechnya lasting several months, while the Chechen Republic has also formed its own OMON detachment. OMON sustained heavy losses in the second conflict as well, including the March 2000 ambush in which more than 30 OMON servicemen were killed (including nine captured and executed), the July 2000 suicide bombing which inflicted more than 100 casualties at the OMON base in Argun, and the April 2002 attack which killed 21 Chechen OMON troopers in central Grozny. Control and discipline is questionable in Chechnya, where the members of the group were noted to engage in or fall victim to several deadly friendly fire and fratricide incidents. In the bloodiest incident at least 24 Russian OMON officers were killed and more than 30 wounded when two units (from Moscow and Sergiyev Posad) fired on each other in Grozny on March 2, 2000. Among other incidents several Chechen OMON servicemen were abducted and executed in Grozny by Russian military servicemen in November 2000, members of the Chechen OMON clashed with the Ingush police on the Chechen-Ingush border resulting in eight fatalities and about 20 injuries in September 2006, and the Chechen OMON clashed with a group of Chechen GRU commandos following a standoff in Grozny resulting in five dead and several wounded in 2007.

In the course of the Chechen conflict the OMON has been accused of severe human rights abuses including abducting, torturing and killing civilians. As of 2000, the bulk of war crimes recorded by international organisations in Chechnya appeared to have been committed by the OMON. An OMON detachment from Moscow region took part in the April 1995 rampage in the village of Samashki, during which up to 300 civilians were reportedly killed in the result of a cleansing operation conducted there by the MVD forces. Two Russian OMON units (from St. Petersburg and Ryazan) were also linked with the Novye Aldi massacre in which at least 60 civilians were robbed and then killed by the Russian forces entering Grozny in February 2000. In 1999 a group of OMON members shot dead around 40 refugees near Grozny. In April 2006 the European Court of Human Rights found Russia guilty of the forced disappearance of Shakhid Baysayev, a Chechen man who had gone missing after being detained in a March 2000 security sweep by the Russian OMON in Grozny. In 2007, the Khanty-Mansi OMON officer Sergei Lapin was sentenced for the kidnapping and torture of a Chechen man in Grozny in 2001, with the Grozny court criticising the conduct of the OMON serving in Chechnya in broader terms. In an event related to Chechnya several OMON officers were accused of starting the May 2007 wave of ethnic violence in Stavropol by assisting in the racist murder of a local Chechen man.

Most members retire at the age of approximately 45 years and receive practically no financial aid from the state afterwards. They are also sometimes not paid for their service (in 2001 for example some 50 OMON members from Moscow filed a lawsuit claiming they were not paid for one month of combat operations in Chechnya). Due to the use of OMON members in high risk situations especially in Chechnya the group often loses members in combat.
Members of OMON are supposed to be extremely fit and experts in small arms and hand-to-hand combat. Males between the ages of 22 and 30 who have completed their two year military service can apply to join OMON (the application includes medical and psychological tests, as well as speed and fitness). The initial training lasts for four months where applicants are extensively trained in the use of different weaponry and close combat, and to follow orders at any cost. Special emphasis is placed on urban combat and entering and clearing buildings. The application procedure closes with a final test where the applicant has to fight three to five trained members of OMON by hand wearing boxing gloves. Fewer than one in five applicants pass and are selected to join.

"Alfa Group" or Group A a special forces (Spetsnaz) or special operations detachment OSNAZ unit attached to the KGB was created on 28 July 1974 within the First Chief Directorate of the KGB on the orders of Yuri Andropov then Chairman of the KGB. It was intended for counter terrorism operations to give the KGB the capacity to respond to such incidents as the 1972 Munich massacre on its own territory. However from the beginning its assigned missions far exceeded its formal scope. The Group was tasked with liberating hijacked airliners within the Soviet Union such as Aeroflot Flight 6833 as well as making sensitive arrests such as that of CIA spy Adolf Tolkachev. Their most notable mission during the Soviet period was the attack on the Amin's palace in Afghanistan on 27 December 1979, the special operation which began the Soviet-Afghan War. The operation involved storming a high hill under extremely heavy fire and lots of intense close combat resulting in the death of the Afghan president, Hafizullah Amin, and his approximately 200 elite guards. In the operation Alfa group lost only two men while the other Soviet forces lost 19. Other governmental buildings such as the Ministry of Interior building, the Internal Security (KHAD) building and the Darul Aman Palace were also seized during the operation, which Alfa group's veterans called the most successful in the group's history. The unit served extensively in the following Soviet occupation of Afghanistan as well.

In October 1985 Alfa was dispatched to Beirut, Lebanon when four Soviet diplomats had been taken hostage by militant Sunni Muslims. By the time Alfa was onsite one of the hostages had already been killed. The perpetrators and their relatives were identified by supporting KGB operatives and the latter were taken hostage. Following the standard policy of 'no negotiation' Alfa proceeded to sever some of their hostages' body parts and sent them to the perpetrators with a warning that more would follow if the Russian hostages were not released immediately. The tactic was a success and no other Russian national was taken hostage in the Middle East for the next 20 years until the 2006 abduction of Russian diplomats in Iraq. During the Soviet coup attempt of 1991 the Alfa group (under the command of Major General Viktor Karpukhin) was assigned the task of entering the White House, Russia's parliament building and killing Boris Yeltsin and the other Russian leaders following a planned assault on the entrance by paratroopers. This order was unanimously refused. Unit members mingled through the crowds and assessed the possibility of undertaking such an operation. According to their statements in the following months it could have been carried out with success and achieved its main objectives within 20 to 25 minutes but would have resulted in hundreds if not thousands of civilian deaths.