Ratko Mladic, arrested in May and transferred to The Hague after 16 years on the run, is accused of orchestrating the genocide of 8,000 Muslim men and boys in Srebrenica in 1995 and the 43-month siege of Sarajevo in which 10,000 people were killed.
Describing himself as a "gravely ill" man when he first appeared in court in June, Mladic defiantly dismissed the charges against him as "monstrous" and "obnoxious" and lawyers for him have also raised concerns about his health.
Worried by Mladic's health and wanting to "maximise the prospect of justice for the victims", prosecutors said they now want to conduct separate trials, dealing with Srebrenica first followed by the siege of Sarajevo and other crimes.
"Trying the Srebrenica indictment first will maximise the likelihood of completing a trial and having a judgment issued," the prosecution said in a court filing dated Tuesday but made public on Wednesday.
The Yugoslavia tribunal has been criticised for the length of its trials after the case against former Yugoslav president Slobodan Milosevic dragged on for more than four years, ending with his death in custody in 2006 and no verdict.
Prosecutors had initially wanted to try Mladic together with his political leader, former Bosnian Serb president Radovan Karadzic, but split the case before the start of Karadzic's trial in October 2009.
In its latest filing, the prosecution said it could present its evidence against Mladic in the Srebrenica trial within one year and be ready to start the second trial when the first is completed.
They said the number of charges against Mladic would remain the same, but splitting the case was a "prudent and practical" step that would not compromise Mladic's rights.