The 7.5 tremor struck at 12.02am near Hanmer Springs and was felt in many parts of New Zealand.
There have been hundreds of strong aftershocks and Civil Defence staff said they would continue to monitor this and update the public if the situation changed.
However, Emergency Management Otago spokesperson for the Waitaki District, Ewen Graham, said over the next 72 hours sea currents could alter, so people needed to exercise caution and stay out of the water.
Earlier, about 19 people had to be evacuated from Waitaki fishing huts on the Waimate side of the Waitaki River.
Waimate District Council Civil Defence emergency management co-ordinator Hilary Botting said fishers were taken to the Glenavy Community Hall shortly after the quake and returned to their huts in South Canterbury about 3.30am.
Civil Defence staff also went to freedom camping areas near Waimate to advise people of the danger, with some leaving and a couple refusing to listen to the warning.
Police this morning cleared the Waihao River of whitebaiters who ignored repeated advice from local Civil Defence staff to stay clear of the water.
Ms Botting said there was a danger that the waterway would be affected by distorted currents caused by the big quake and people needed to put their safety first over their desire for whitebait.
"You can have some quite significant currents running up and down the coast for a day or two."
Sergeant Kevin Reynolds, of Waimate, confirmed that some whitebaiters were choosing to stay at the river.
"Some are not heeding the warning to stay out of the water which is a little concerning."
State of emergency lifted in Dunedin
The 7.5 quake was followed by a series of strong aftershocks, triggering a tsunami alert down the length of the east coast of the country. The alert was downgraded to a marine and beach threat and about 12.30pm the threat to the Otago region was lifted.
Dunedin Civil Defence had lifted the state of emergency issued early this mornng in response to the tsunami threat. People who evacuated from low-lying coastal areas were allowed to return home.
There had been no reports of damage from the 7.5 quake in Dunedin, but people should be cautious about going on beaches.
Earlier, police moved campers from Brighton, and in Dunedin a steady of people were evacuated to higher ground, including the St Clair Golf Club and Unity Park in Mornington. Police were at St Clair and St Kilda beaches warning people to stay away.
In South Otago, the Owaka Community Hall was opened as a welfare centre for those evacuating low-lying coastal areas.
'Complex' quake
Geonet duty seismologist Anna Kaiser said Monday's quake sequence was "looking complex" and may involve more than one fault. Investigations were under way but there was a still a lot to learn about what had happened.
"We're working very hard." The epicentre was possibly just south of the Hope fault, but it did look like "something else was going on".
Aftershocks were occurring up the east coast of the South Island, which was a complex area of faults, Dr Kaiser said.
"We don't know what we are dealing with right now but it may be ... it involves potentially more than one fault ... we need to figure out what was going on before and after the [7.5 magnitude] quake."
New Zealand lies in the seismically active "Ring of Fire", a 40,000km arc of volcanoes and oceanic trenches that partly encircles the Pacific Ocean. Around 90% of the world's quakes occur within this region.
