According to a government statement released on Sunday, Milorad Lukovic Legija turned himself in to authorities.
"Serbian Interior Minister Dragan Jocic announced that this evening, 2 May, at 19:00 GMT, Milorad Lukovic Legija, the top person charged in the case of the murder of Serbian prime minister Zoran Djindjic surrendered himself to Interior Ministry forces," said the statement.
"Lukovic has been arrested and legal proceedings are underway," it added.
Lukovic, an ex-chief of the Red Berets secret police unit who is better known as Legija, is accused of masterminding the 12 March 2003 assassination along with fellow crime boss Dusan Spasojevic.
Key anti-Milosevic figure
Djindjic's murder shook the country and hastened the disintegration of the moderate alliance which had ruled Serbia since former Yugoslav president Slobodan Milosevic was toppled from power in 2000.
A key figure in the anti-Milosevic movement, Djindjic had stirred up a range of enemies with his decision to extradite the former strongman to the UN war crimes tribunal at The Hague in 2001 and his efforts to crack down on organised crime.
Lukovic and 12 other criminal gang members have been on trial for Djindjic's murder since February. Seven of them, including Lukovic, have been tried in absentia.
According to charges read out in court at the opening of the trial, the alleged ringleaders planned to seize power on behalf of a shadowy group of conspirators.
The indictment said alleged mafia bosses Lukovic and Spasojevic had "created a conspiracy with the goal of executing criminal acts against the constitutional order and the security" of the country "with the goal of achieving profit and power."
The indictment added that their plans included the "killing of the prime minister of Serbia and other officials" to create a "feeling of insecurity among citizens".
A former Milosevic ally and a veteran of the Bosnian and Kosovo wars in the 1990s, Legija profited from the blurring of lines between politicians, the security forces and crime gangs which was common during Milosevic's rule.
The second alleged ringleader, gangster Spasojevic, was killed in a confrontation with police in Belgrade on 27 March.