The Wellington harbourmaster says he expects the city's port company to look at options for preventing empty containers being dumped in the harbour by high winds.
Three containers landed in the sea on Friday.
Two have been recovered and the third will not be recovered until tomorrow.
Wellington harbourmaster Mike Pryce said dive teams would use airbags to refloat the third container in the morning.
Mr Pryce said before the 2013 Seddon quakes, there was a road running behind the stacks of containers.
But he said it partially collapsed in the quakes and when the port company built an underwater seawall it pushed the land in further.
Mike Pryce said, in the past, the roadway would have captured falling containers.
He expected CentrePort will conduct an investigation and to consider mitigation measures.