The skipper then steered the boat back out to sea and the vessel immediately stopped taking on water.
Once the Coastguard Papakura rescue boat reached the fishing boat it took the two children onboard.
The Coastguard Waiuku rescue boat then led the fishing vessel and the other Coastguard boat to a calmer part of the bar, where they all crossed safely back.
The Auckland Rescue Helicopter also assisted with the rescue of the troubled boat on the Manukau Harbour by circling the fishing boat while the water rescue boats crossed the bar to reach it.
There were no injuries.
Coastguard said the incident is just another example of how unpredictable the Manukau Bar is.
Last month, four people were saved from a sinking boat in the Manukau Harbour. They were clinging to the bow of the boat that was just poking above the water when they were spotted by the Auckland Westpac Rescue Helicopter crew.
A police spokesperson said it was a "good thing" the five people onboard the boat on Wednesday were wearing lifejackets, but reminded people to check the weather forecast before hitting the water.
"The weather conditions were not great at the time, and we encourage and remind boaties to check the conditions before going out on the water and strongly consider delaying your journey if the weather conditions are rough and large swells are reported."
Safety tips for crossing the Manukau Bar
• Always check the swell, tide and wind conditions – every crossing of the Manukau Bar is different because of these factors.
• Always try and cross the bar during daylight hours.
• Make sure that everyone on board is wearing a lifejacket and are awake.
• Crossing at high tide is best (but always take the weather and swell into consideration too).
• Ensure that you are carrying two forms of communication that work even when wet.
• Log a bar crossing report with Coastguard by calling *500 on your mobile or contacting Coastguard radio from your VHF. Once over the bar safely close your bar crossing report.
• If in doubt, don't go out!
Source: Coastguard