The category four storm caused widespread flooding and damage to homes across the country.
With the full extent of the damage yet to be determined, authorities are urging the public to remain indoors until given the all-clear.
Misa Funaki, of the Fiji Meteorological Service, said communication networks were down in the outer islands, including Kadavu, which felt the brunt of Harold.
"Reports are coming in on the devastation caused by Harold - not only on the main island of Viti Levu but moreso in the maritime islands of the Lomaiviti and Lau groups," he said.
"Reports are coming in of the damage - of houses being ripped apart and of storm surges in the remote islands."
Mr Funaki said a major clean-up was underway with police and military clearing debris and keeping people away from flooded rivers and towns.
The last time Fijians hunkered down from a natural disaster of such magnitude was in February 2016 when Cyclone Winston - a category five storm - made landfall.
Winston was the most strongest cyclone in the southern hemisphere and inflicted extensive damage across Fiji killing 44 people.
On Wednesday, Cyclone Harold grazed Fiji's south-western and southern parts with flooding reported in Suva, Tavua, Ba and Lautoka.
But the most damage, authorities said, was received by Kadavu.
The village of Naioti, in the district of Yale, felt the full brunt of the storm.
Homes were flattened and debris scattered throughout the village.
Communication networks in Ono, Naqara and Naikoso were also down.
The government said full assessment of the damage in Kadavu, southern Lau and smaller islands nearby was being carried out.
In Nausori, roofs were blown away in what some residents said was a "freak-tornado".
Rajesh Singh said it took them by surprise and was the worst thing he had experienced. He said homes in the area were inundated with water.
In the capital Suva the military had begun clearing debris.
Meanwhile in the north of the country, food gardens were damaged, including farms.
The Ministry of Health advised the public to boil all drinking water.
Chief Medical Adviser Jemesa Tudravu said given the impact Cyclone Harold had on water supply, there was a need to ensure every precaution was taken.
"We have high risks of the spread of infectious diseases such as typhoid and leptospirosis so we should be boiling all drinking water."
Meanwhile the Ministry of Education had begun its assessment of the damage to schools around the country.
But Cyclone Harold was only part of the challenge faced by authorities in Fiji.
Fiji has 15 confirmed cases of Covid-19 and hundreds are in isolation for 14 days.
With lockdown and curfew restrictions in place, the public had been urged to adhere to the government directives in particular "stay and home exercise social distancing".
Prime Minister Frank Bainimarama called on all people in Fiji to remain indoors until the all-clear was given by authorities.
Mr Bainimarama said heavy rain and flooding would continue even after Harold left the country.
"I am pleading with Fijians to stay out of the floodwaters. Keep your children out of floodwaters. These waters are deadly, unpredictable and can carry debris that can maim or kill."
He said the capital Suva was on lockdown but people could be seen "out and about", despite reports of winds whipping up and throwing debris around the city.
He said the government had also received reports of vendors and farmers trying to sell their produce.
"This must end. Everyone must immediately shelter indoors, in their homes or evacuation centres.
"Flying debris can be deadly."
The National Disaster Management Office had activated more than 80 evacuation centres across the country with almost 2000 people sheltered there.
NDMO director Vasiti Soko said they were monitoring the centres to ensure social distancing was observed.
Ms Soko said people would remain at the centres until the all-clear was given.
During the height of the storm, patients at Lautoka Hospital were evacuated.
Police and the army helped evacuate residents from flooded homes in the western division.
Health officials have urged those at the centres to ensure hygiene is maintained, social distancing is practised and to refrain from any social gatherings.
The restriction of movement has been eased with businesses open but the government said Covid-19 restrictions and the curfew which starts at 8pm tonight, remained in force.