One 5.1 jolt yesterday, centred just off Lyttelton, rattled those working at the port, particularly two men in a crane on a 1m-wide platform, more than 50m above ground.
Lyttelton Port Co chief executive Peter Davie said staff were working to reinforce structures.
Damage was estimated at $50 million, he said.
"For us, the port is about months and years of restoration work. There's no quick fix for a lot of the work."
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Among the damage was a lighthouse, which staff had nicknamed "the leaning tower" because of its new angle.
There were also deep cracks in the ground, which had been worsening with each aftershock.
Norman Eyre (44) and a 24-year-old apprentice had just climbed up a crane to repair damage caused in Saturday's 7.1 quake when the 5.1 magnitude tremor hit, shortly before 8am.
"We got to the top platform, had a huff and puff and put down all our gear, and then the whole thing started violently shaking.
"We would've been 50m or 60m in the air, and the platform is about 1m by about two feet, so we could have fallen off," he said.
"We sort of looked at each other and thought `Gee, is that an earthquake or has something hit us?'," he said.
"We were looking down and could see cracks opening up even further. One of the vehicles tried to leave and [it] actually fell down one of the cracks."
They came down for an hour while the port was evacuated, but then resumed work.
"A couple of people said to me 'Don't you feel a bit shaky going back up', but, you know, we've been living between the shakes since Saturday," Mr Eyre said.
Mr Davie said the quake had caused a fair amount of unease among staff.
"They are nervous, and understandably so, but we keep putting our engineering staff in front of them and reinforcing that the structures there are built to withstand these type of things."
Transport Minister Steven Joyce, who visited the port yesterday, said the extent of the damage was dramatic.
"The sheer force of it, when you get up close to it ..." he said.
Port Otago chief executive Geoff Plunket said the damage to the Lyttelton port was having no impact on Port Otago's operation, nor its 15.8% shareholding in the company.
"They are able to manage it themselves. They have no need for any extra support."
