After two years of teaching, Makarov entered public service, first as the chairman of the presidium of Sovietskii rayon (1990-1992) and later as the head of the Sovietskii raion administration (1992-1996). In 1994, he also ran for and won a seat in the Tomsk Oblast duma. His seat in the duma became a springboard for his run for the mayorship of the city in 1996. Makarov defeated Aleksandr Konovalov that year and won re-election in 2000 and 2004. From 1996-2001 he served simultaneously as mayor and as a duma deputy.

During the search of his home, Makarov suffered a heart attack and was transported to the hospital. Legal proceedings have been suspended while he is being treated. However, the prosecutor, Sergei Panov, is now considering further charges, alleging that Makarov has made threats against investigators.
Panov has also alleged that the mayor's condition is sufficient to allow the trial to move forward. (in Russian)
Makarov's attorney, Natalia Azurova, has protested to the court that the prosecutor's actions are illegal. Specifically, she claims that searches were conducted at the homes of his children, that sums of money found were not in the "eight figures" claimed by prosecutors and that no actual witnesses have stepped forward.
On December 26, 2006 further charges were levelled against him by the prosecutors office after it was claimed that the police found large amounts of opium in his apartment.