Titti Postiglione, a spokeswoman for the Civil Protection Department, said: "In the next few hours the Tiber river will overflow north of Rome, in the areas that are usually subject to flooding.
"So we organised small scale evacuations, we are keeping them under control, and it [the wave of high water] is moving slowly towards the centre of the city."
The authorities say the next several hours will be "critical".
"I have never seen the river at a level this high - today it is really swollen"
Alessandro Freza, resident of Rome
Hundreds of residents have been evacuated from their homes near the Tiber and emergency services have sealed off the area around the historic Ponte Milvio pedestrian bridge.
The Civil Protection Department warned the Tiber had already risen by about 4.9 metres in the past two days alone.
Firefighters in dinghys and trucks travelled through the flooded areas rescuing stranded people.
Alessandro Freza, a resident of the city, said: "I have never seen the river at a level this high, today it is really swollen, but there is still another margin of five to six metres so we must keep hoping."
Most of Italy has been hit by extreme weather in recent days, with heavy snowfall blanketing the north and strong winds and downpours lashing the south.
The flooding has already claimed the lives of at least four Italians.
On Friday, rescuers recovered the body of a man in southern Italy who was swept away in heavy rains, another died after his car was hit by a tree and another was killed in a car crash in a rainstorm.
A woman died in her car after it become submerged in an underpass in Rome on Thursday.
Officials in other Italian cities also called for a state of emergency to be declared in the worst hit areas.
Earlier on Friday, thousands of workers, students, pensioners and unemployed braved the heavy rain to march through cities to protest against the government's handling of the economic crisis.
The daylong general strike by CGIL - Italy's largest union - curtailed services at hospitals, schools, banks and post offices.
Demonstrators waved banners reading "united against lay-offs" and "more jobs, more wages, more pensions, more rights".
The Italian centre-right government, lead by Silvio Berlusconi, dismissed the strike by the left-leaning CGIL union as politically motivated and said it would further damage the economy - which is slipping into recession along with most of Europe.