A strong 5.9-magnitude earthquake rattled New Zealand on Friday, seismologists said, panicking shoppers but prompting no reports of any major damage.

The quake hit at 3:36 pm (0336 GMT) with its epicentre about 66 kilometres (41 miles) from the South Island town of Kaikoura at a depth of 55 kilometres, the US Geological Survey said.

The local GeoNet monitoring service measured the quake at 6.3 and said it was felt across the entire country, but was unlikely to cause damage because of it was so deep.

Kaikoura District Council chief executive Stuart Grant told TVNZ if felt like two tremors in quick succession, describing the second of them as a "big jolt".

He said the council building was evacuated as a precaution but appeared undamaged.

The manager of Kaikoura's Mitre 10 hardware store James Hills said the quake dislodged items from shelves and sent panicked customers fleeing from the building.

"(There was a) fair bit of panic... everything was falling off the shelves," he said.

"There's been a little bit of damage, certainly not heaps, but yeah, there's a lot of stuff fallen over."

The quake struck in the same region as a 4.7 tremor on Thursday that jolted office buildings in Wellington.

New Zealand is on the boundary of the Australian and Pacific tectonic plates, which form part of the so-called "Ring of Fire", and experiences up to 15,000 tremors a year.