Posters outside the church in the east of the city declared Vittorio Casamonica the "King of Rome", while mourners were greeted with music from the film "The Godfather".
Read more: Outcry as mafia boss given lavish send-off
Interior Minister Angelino Alfano and Rome's mayor Ignazio Marino said they were furious at the defiant spectacle, with the city's police chief admitting Friday to "a failure in the system".
"It is intolerable that a funeral should be used to pass mafia messages," Marino said on Twitter.
Ho chiamato il Prefetto perché siano accertati i fatti. È intollerabile che i funerali siano strumenti dei vivi per inviare messaggi mafiosi— Ignazio Marino (@ignaziomarino) August 20, 2015
Although he was never convicted of being a Mafia don, the 65-year-old - who died of cancer - was the alleged head of Casamonica clan, which reportedly runs drugs, fraud and extortion rings in Rome.
The clan - which has its roots in the Roma community - is one of crime networks accused of infiltrating the city's government and influencing politicians in a spiralling corruption investigation.
The day before Thursday's funeral a judge had set the date for the trial of 59 people charged in relation to graft around the awarding of city contracts.
The gaudy event has gone down particularly badly because in 2006 the same church refused a funeral to the terminally ill poet Piergiorgio Welby, who was helped to die by one of his doctors in a case that divided Italy.
But the new priest in charge of the church said he knew nothing of Casamonica's past, or of the pomp his friends had planned for his send-off.