The incident has affected traffic on Cross St, The Strand and Tapora St.
"One person is critical and the serious crash unit is investigating," a police spokeswoman said.
Meanwhile, motorists driving between Wellington and the Hutt Valley are being told to expect delays due to a slip on SH2.
The NZTA said it's blocking the left northbound lane, north of the Hutt Road on-ramp.
Heavy rain has fallen in the capital in the past 24 hours with Wellington City Council contractors called to reports of flooding, dancing manholes and blocked sumps all over the city.
A council spokeswoman said they've been working overnight to get everything fixed for the morning commute.
Last night trains were suspended for an hour between Khandallah and Johnsonville due to flooding.
The Night Noodle Market also had to be closed due to rain flooding the Basin Reserve.
Organisers apologised in a Facebook post, saying their number one interest is ensuring the safety of visitors.
A decision on whether tonight's market can go ahead will be made this morning.