"For today, we're expecting wave heights to reach four to four and a half metres."
The heavy swells will combine with high tides in the city and the south coast between 11.45am and 12.50pm.
Riptides could be stronger than usual, increasing the chances of people in the water getting in trouble, Makgabutlane said.
"We do urge people to be extra careful with these heavy swells."
The heavy swell warning is valid until 7pm.
The intense Sunday weather conditions come after weeks of gloomy weather in the capital.
Storm-force winds up to 130km/h battered parts of Southland and Otago earlier this weekend before moving north.
MetService expected a cloudy Monday morning in Wellington, with a few showers developing in the afternoon.
Southerlies were likely to peter out in the morning, MetService said.
Many parts of eastern New Zealand will experience cooler than average temperatures today.
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MetService said showers would linger in the North Island's eastern flank until clearing later today.
The main low-pressure system on Sunday morning was just south of the Chatham Islands and moving eastwards as high pressure expanded from the west.
WeatherWatch forecasters said the capital's cloudy weather would continue for several days in the week ahead.
"While this low may not bring gales at first to Wellington, it may leave a sting in its tail with a burst of strong-to-gale southerlies later this week and into the weekend," WeatherWatch added.