Super typhoon Megi has slammed into the northern Philippines, cutting off power, forcing airlines to cancel flights and putting the region's rice crop at risk.

Forecasters said Typhoon Megi is the strongest storm to hit the Philippines since Typhoon Durian unleashed mudslides that buried entire towns and killed over 1,000 in 2006.

It is one of the most powerful storms recorded in the world this year.

The northeastern provinces of Isabela and Cagayan were the first to feel the typhoon's fury this morning.

Megi hit Isabela province at 11.25am local time and is heading across the north of the main island of Luzon with winds of 225km/ph near the centre.

Officials have warned of rough seas and the risk of flash flooding, storm surges and landslides.

'We expect it to weaken and slow down after slamming into the mountains,' Mario Palafox, a senior forecaster told reporters.

Mr Palofox said the typhoon's eye had shrank to about 50km but is expected to bring more rain and stronger winds.

Isabela and other provinces in Megi's direct path are mostly agricultural and fishing areas, with a few million residents who are well-drilled in preparing for the many storms that hit each year.

Over 3,000 people have already been moved from their homes in the northern provinces as part of a 'pre-emptive evacuation' of threatened areas.

Flights to and from northern Luzon have been suspended and ships have been told not to leave port.

Last year, the country lost 1.3m tonnes of paddy rice following three strong typhoons in September and October, prompting it to go to the market early to boost its rice stocks.

'This could bring destruction to our crops,' Val Perdido, a regional farm official, told reporters.

Agriculture department spokesperson Andrew Villacorta said Luzon's Cagayan valley accounts for 12% of national rice output, or about 1m tonnes of unmilled rice, lower than earlier estimates from local officials.

'Isabela and Cagayan are expected to be hit hard,' Mr Villacorta said.

'Our estimates showed about 159,000 metric tonnes will be lost from Isabela. About 88,000 hectares will be affected.

'In Cagayan province, about 43,000 hectares will be affected. The estimated loss will be around 63,000 metric tonnes.'

He said just over one third of the crop had been harvested, while about 90% of the corn crop had been harvested.