There are so far no confirmed reports of deaths, but officials said at least three people were injured and up to 40 per cent of homes damaged.
Leweniqila said crops on both islands had been damaged, but Fiji's most populated centres escaped serious harm as Cyclone Gita passed south of Fiji's capital, Suva.
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He said the primary islands of focus include Ono-i-Lau, Vatoa, Ogea, Namuka, Fulaga, and Kabara - which combined hold a population of 1,579 people.
Reds prop Taniela Tupou has issued an emotional plea for help after his family's house was destroyed in Cyclone Gita.
Lt. Gov. Lemanu Peleti Mauga says the storm caused widespread damage to homes and infrastructure.
Tonga could take six months to recover from what's being called the worst storm there in 60 years, while almost half a Fiji island's residents are still in evacuation centres.
It is expected intensify to a category five cyclone as it passes over the Ono-i-Lau group of islands.
Chris Brandolino, a scientist at New Zealand's National Institute of Water and Atmospheric Research, said flooding and coastal inundation would likely cause as many problems in Tonga as the damage from the winds.
Martens said the cyclone was now south of the main Fiji island of Viti Levu and would travel west over the next 48 hours to just below New Caledonia.
"A lot of the old heritage buildings, some that have stood for over 100 years, have been destroyed".
About 2,500 people living on two of Fiji's islands were at risk, the nation's National Disaster Management Office told Radio New Zealand.
Meanwhile almost half the residents of Fiji's Ono-I-Lau island are in evacuation centres because their homes were so badly damaged by Cyclone Gita.