It is the first time the city has allocated money to tackle this crime.
Gillison said the city wanted to make sure the program had stable funding.
Many criminals are poor and unlikely to pay fines, and even if they did, it would have taken years to build a substantial sum that way.
"The mayor felt that if you're going to try to help people," Gillison said, "let's help them now."
The money will come from his office, and Gillison said he was reviewing his budget to identify funding sources.
The city said it would give the money to District Attorney Seth Williams.
Williams said he would use the money to help relocate witnesses facing threats.
"Witness intimidation is a serious thing," Williams said. "There are people being threatened every day by cowards and thugs who want to stop the criminal justice system by stopping witnesses from testifying."
Jones said he wanted to make fighting the problem a top priority for government officials.
"More important than the money . . . it's elevating the issue that's the most important thing," said Jones, citing State Rep. Brendan Boyle's new bill that would create a statewide witness-relocation program, along with a witness-protection bill introduced in the U.S. Senate by Sen. Arlen Specter, (D., Pa.)
In a series published in December, The Inquirer reported that Philadelphia had one of the nation's lowest felony-conviction rates and that a key reason was that witnesses were often terrified.
Williams, working with top police commanders, has revamped investigative procedures and launched a crackdown on perpetrators. Judges also have been working to eliminate witness intimidation in their courtrooms.
Lawmakers in Congress, the statehouse, and City Council have introduced proposals to provide more money for relocating witnesses and to make witness intimidation in state court cases a federal crime.
