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The mayor of Christchurch, Bob Parker, told the BBC Christchurch residents were "very nervous"
A second quake, magnitude 6.0, struck an hour and 20 minutes later, shaking buildings and causing injuries.
Information is still coming in about the extent of damage; boulders have been reported tumbling down hillsides.
A week, ago Christchurch was also hit by two shocks which cleared shop shelves and increased nervousness in the city.
A total of 181 people died in the 6.3-magnitude quake in February, which also destroyed hundreds of buildings.
Mayor Bob Parker told Radio New Zealand there were new fears for Christchurch Cathedral.
"Thank God we had evacuated the red zone," he said, in a reference to the centre of the city which remains closed off.
"We are being enveloped with dust. It is very very scary.
"There has been a report of a further collapse of the remnants of the Christchurch Cathedral.
"We need to get a picture of what is really happening and to make a call on where we need to send our essential services."
The Christchurch Press reported a building had collapsed, with some people believed to be trapped inside.
An inquiry into the collapse of one of the buildings destroyed by the devastating 22 February earthquake opened on Monday and was briefly evacuated following the latest shakes.
About 10,000 houses and nearly 1,000 commercial buildings will have to be demolished as a result of the February quake.
Recovery and reconstruction costs are expected to total at least NZ$15bn ($11bn; £7bn).
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