The prosecutor dropped more serious abuse of office charges against the city's first female mayor, a member of the populist Five Star Movement (M5S).
But a judge will now have to decide if Raggi should appear in court to answer charges that she lied to the head of the city's anti-corruption watchdog when she told him she had personally appointed Renato Marra as the town hall's tourism chief.
Investigators suspect that Marra was actually given the job by his brother Raffaele – currently on trial for corruption – a former close aide to Raggi.
The prosecutor said an investigation into another Raggi appointment that had been linked to insurance policies taken out in her name by the successful candidate should be shelved as there was no evidence of her having committed any crime.
Raggi welcomed that element of Thursday's announcement. “For months the media has been speaking about me as if I was a criminal but now they owe me and the citizens of Rome an apology,” she wrote on her Facebook page.
M5S has emerged in recent years as Italy's biggest opposition force and polls suggest it could become the largest party in parliament after an election due in the first half of next year.
Raggi's election in June 2016 was a major coup for the party but her administration has been dogged by scandals, delays in forming a team and little signs of progress in dealing with Rome's problems of failing public services and crumbling infrastructure.