An Air New Zealand spokesman said five services bound for Napier had been cancelled, along with four services out of Napier.
Road travellers heading in and out of Auckland have also faced extended delays.
Senior sergeant Jonathon Chappell, speaking to Newstalk ZB at the Mercer checkpoint, said 23,000 vehicles had been through the five checkpoints on Auckland's southern border since the start of the lockdown.
In 22 hours, only 320 vehicles had been turned back for either not having a legitimate reason for travelling or not having the required paperwork.
Business Hawke's Bay CEO Carolyn Neville said any disruption to supply chains will have a flow-on effect to businesses throughout the region.
"There will be many in Hawke's Bay waiting for essential items coming via freight including manufacturers and exporters," she said.
"Hawke's Bay businesses that are waiting on freight should be in touch with their freight company and customers and do their best to manage expectations."
Foodstuffs head of corporate affairs Antoinette Laird said the implementation of regional borders caused some initial delays with deliveries leaving and passing through the Auckland region.
"Our teams know what to do and have pulled together once more to make sure customers experience no impact at their local Foodstuffs supermarket as a result of the roadblocks," she said.
The travel disruptions also meant Hawke's Bay Today and NZ Herald newspaper deliveries into the region were held up this morning due to long delays at the Auckland border patrol.
The newspapers are printed at the NZME Ellerslie print site and trucked to Hawke's Bay.
Neville said the organisation feels for Auckland businesses and those who have been affected through the lockdown.
"Hopefully the delays at the Auckland borders at the weekend were reflective of short notice given for this lockdown, and not reflective of business as usual at the border," she said.
The Royal New Zealand Ballet's national tour of Tutus on Tour, due to be held at Toitoi Hawke's Bay Arts & Events Centre on March 2, has been postponed.
Performances in New Plymouth, Whanganui, Gisborne, Tauranga and Nelson have also been postponed.
Basketball Hawke's Bay also announced the cancellation of the Napier Year 1 and 2 Competitions due to be held on March 4.
The cancelled Te Mata Kindergarten Junior Triathlon and Family Picnic has been postponed until March 14.
Central Football - Hawke's Bay said their futsal competition will go ahead at Mitre10 Park Hawke's Bay, but with adjustments to protocol.
All teams must wait outside the entry gate before entering the fields five minutes before kick-off, one spectators and two coaching staff will be allowed per team and players must bring their own drinks bottles.