The airport put the fog restrictions in place at 4.39am.
It comes after 60 flights were affected by fog yesterday, including 28 cancelled and 32 delayed, with restrictions lasting until 9.47am.
MetService meteorologist David Miller said the fog had set in about 4.30am, but should clear by mid-morning.
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There were also reports of fog in Hamilton, and earlier this morning in Wellington.
The fog was a result of rain over the past few days, and still nights.
"In Auckland the fog is being caused by some lingering moisture, with nothing to push it out. Showers and strengthening westerlies later today will change that."
Once the fog cleared Auckland was in for a showery day and a high of 17C.
Meanwhile, a low pressure system that hammered the Gisborne area yesterday has pushed further south, bringing rain to the lower North Island.
Weather stations in the Gisborne ranges recorded close to 100mm of rain yesterday, while on the flats there were recordings of 50mm.
Wellington and Wairarapa south of Featherston were under a heavy rain watch to 6pm tonight. Much of the North Island would see at least some showers today.
The South Island was in for relatively "benign" weather, with just some low cloud and drizzle in the east, Miller said.
Saturday would be the pick of the weekend, with mostly fine weather forecast across the country before a front moved in on Sunday bringing burst of heavy rain to the western parts of both main islands.
During Sunday and Monday, a showery and cold west to southwest flow would spread over the country.
Snow could lower to about 300m over Southland and Otago.
A deep low should pass to the south of the country during this time, with potential for severe southwest gales about Southland, Clutha and Dunedin.
On Tuesday, a ridge would develop over the lower South Island, while cold southerlies persisted over central and northern New Zealand.
Today's weather
Whangārei
Few showers, more frequent from afternoon with heavy falls and chance thunderstorm. Northwesterlies. 17C high, 7C overnight.
Auckland
Few showers, chance heavy from afternoon. Westerly breezes dying out. 17C high, 6C overnight.
Hamilton
Chance early fog, then one or two showers, clearing by evening. Light winds. 16C high, 4C overnight.
Tauranga
Few afternoon showers. Westerlies dying out. 17C high, 6C overnight.
New Plymouth Fine. Southeast breezes. 15C high, 5C overnight.
Napier A few spots of rain, clearing this afternoon. Southwesterlies. 18C high, 3C overnight.
Whanganui Occasional rain, easing evening. Southwesterlies, strong at times. 15C high, 6C overnight.
Wellington Periods of rain, gradually clearing tonight. Strong southerlies, gale gusting 90km/h in exposed places. 12C high, 7C overnight.
Nelson Fine. Southwesterlies. 15C high, 3C overnight.
Christchurch Becoming cloudy this morning, drizzle at times. Strengthening southwesterlies. 11C high, 4C overnight.
Dunedin Low cloud and fog with occasional drizzle. Southwesterlies, strong about the coast in the evening. 10C high, 6C overnight.
