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Golf ball-sized hail has fallen on parts of Sydney after a wild afternoon storm swept through.

Other parts of NSW including Singleton and Warragamba also copped hailstones.

Darkness fell over the city around 3.30pm as the weather swept through.

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Alerts were issued ahead of the storm, with warnings of flash flooding and damaging wind and hail.

The Bom says 5cm hail was recorded at Penrith at 4pm.

A gust of 91 km/h was recorded at Western Sydney Airport at 3.42 pm.

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A weather warning remains in place for "very dangerous thunderstorms" in Central Tablelands and parts of the Hunter, Metropolitan, Illawarra, Southern Tablelands, North West Slopes and Plains, Central West Slopes and Plains, South West Slopes and Riverina Forecast Districts, the BOM says.

"Severe thunderstorms with heavy rainfall, and possible damaging wind gusts and large hail continue," it says.

A cleanup is under way in Far North Queensland after Tropical CycloneNarelle swept over the Cape York Peninsula, narrowly missing populated communities.

Queensland Premier David Crisafulli said the tropical cyclone left the east coast of Cape York, just south of Aurukun overnight, delivering "sizeable winds and some pretty reasonable rain" despite being downgraded to a category 2 system.

"It walked a tightrope perfectly between Coen and Lockhart River, and then ducked just south of Aurukun as it exited on the western side of the Cape," Crisafulli said.

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"That was the best of both worlds on both sides of this part of Queensland.

"The fact that it went right between two of the larger populated centres was a real blessing."

In Lockhart River wind gusts reached 115 km/h, bringing down sodden trees and sending branches flying.

Wind gusts up to 109 km/h were felt in Weipa, along with rainfall totals of 217mm overnight.

"We have reports of some waves of over five metres off the coast of Weipa and we're also getting some more intel today as we go," Crisafulli said.

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He said up to 400mm of rain has fallen in parts, swelling creeks and rivers.

No significant injuries have been reported.

Despite the system passing Queensland, a flood watch still exists for a large part of north and Far North Queensland.

Crews are now working to clear minor structural damage, fallen trees and fix power outages.

Authorities have warned it may take some time to get food and fuel to isolate communities after flood water cut travel by land, leaving the Cooktown airport as the only way to get people and supplies in.

There is significant damage on Peninsula Development Road.

"It could have been far worse, but there is some significant road damage that we will have to swiftly reconnect," Crisafulli said.

"That is a really important road for Far North Queensland. It's important that we get on and do that."

Energy Queensland and Energex crews are on the ground in Weipa, Lockhart River and Coen, Crisafulli said.

Three emergency service helicopters are surveying 16 communities from the air today.

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A boat that went missing in Princess Charlotte Bay during the cyclone has made contact with emergency services and is safe, according to reports.

A decision on whether schools will be reopened will be made by 5pm tomorrow and posted to the disaster.qld.gov.au website.

"But overwhelmingly, based on the size of the system, we couldn't have asked for a better deal out of this," Crisafulli said.

Queensland is now assisting the NT with storm clean-up equipment.

Narelle is expected to lash the Northern Territory as a severe weather system this evening after intensifying over the Gulf of Carpentaria overnight.

Narelle is forecast to intensify again to a category 3 system above Groote Eylandt around 1am before crossing the eastern Top End coast, most likely between Birany Birany and Numbulwar.

Destructive winds up to 185 km/h and major rainfall are forecast for those areas.

Groote Eylandt and potentially Nhulunbuy and Nathan River could be lashed by 160 km/h winds, coupled with heavy rainfall and flash flooding.

The system will then gradually weaken to a category 2 and 1 as it moves inland across the Top End tomorrow and on Monday.

Katherine residents are on flood alert for the second time in weeks, with Narelle's path tending towards the town.

The Katherine community endured major flooding two weeks ago after the Katherine river reached its highest level in nearly 30 years.

Authorities are warning the river could again rise rapidly across the course of tomorrow afternoon and evening.

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