Dragoslav Ognjanovic, 57, was killed on Saturday evening outside his apartment building in the capital, Belgrade.
His 26-year-old son was also wounded in the shooting, the interior ministry said in a statement.
Mr Ognjanovic served on the legal team for Mr Milosevic during his trial at The Hague in the early 2000s.
The former president of Serbia was arrested in 2001 and held at the UN war crimes tribunal for genocide and other war crimes.
But he was found dead in his cell in 2006 before his trial could be completed.
He was facing three indictments relating to atrocities carried out in Kosovo, another for crimes in Croatia, and the third alleging genocide in Bosnia between 1992 and 1995.
In a statement, the head of the Bar Association in Belgrade said the shooting of Mr Ognjanovic was an attack on all lawyers.
“[We will] exert maximum pressure on the competent state authorities in order to find the perpetrators of this crime,” Viktor Gostiljac said.
Mr Ognjanovic also served as a defence lawyer in several high-profile mafia cases in Serbia and Montenegro.
A number of prominent members of Serbian and Montenegrin organised crime networks have been killed in Belgrade in recent years.
Police say the killings are part of a gang war over the illegal drugs market.