More than 100 people reported it as feeling "strong" while seven said it felt severe where they were.
Three people said it felt "extreme" when it hit.
Short and sharp quake
"Short, sharp and shallow for Christchurch this morning," GeoNet said.
"That quake was only a magnitude 3.8 but at 7km depth under Lyttelton Harbour, which is why 6000 of you Cantabrians across the city and Banks Peninsula felt it!
"Most people felt it as a light quake, but it was much stronger around Lyttelton."
Many residents took to social media to report that they felt it.
Grant Shimmin said on Twitter: "That was a wee shake! Walking downstairs and felt the whole apartment rattling."
Another local said it "scared the crap out of me" early this morning.
A woman in Waltham said it felt "very strong" there, as did a woman in St Albans.
By 7.15am, four smaller quakes had been recorded in the South Island since the initial bigger jolt early this morning.
At 6.55am, a 2.8 magnitude quake, categorised as "weak" struck 10km southeast of Christchurch at a depth of 11km.
The other "unnoticeable" quakes hit northeast of Milford Sound, northeast of Mt Cook and northeast of Motueka.