Brigadier Jim Bliss, Head of Managed Isolation and Quarantine, said MIQ was "saddened" to hear of the death during a "medical incident."
He said staff on site and ambulance staff did their best to treat the man.
Support is being offered to all those in the facility including the 155 other RSE workers who arrived in New Zealand with the man yesterday.
"We are doing all we can to assist these RSE workers who are on their first day of 14 in managed isolation and who no doubt will be finding this very upsetting. Our thoughts are with them and his family. Staff on site at the Crowne Plaza are providing support to all those who require it," Bliss said.
Vanuatu consul-general in Auckland, Consul General McKenzie Kalotiti, said the man was one of 150 men linked to the Recognised Seasonal Employer scheme who had arrived in Auckland yesterday afternoon.
"They just came yesterday and at about 8 o'clock, the [group] manager rang me last night to say someone had died.
"He's collapsed there and they pronounced him dead on the spot."
Kalotiti said the 44-year-old victim's family had since been told of the tragedy and extra support calls were being made to those inside the managed isolation facility still.
"The employer, for starters, is really shocked and we are all sad about this.
"We can't predict what happens - it's his first day back in New Zealand and he's died. Such is life."
This is the second death in MIQ in under two months.
In late December, Reverend Samata Iusitini Leiloa died at the Millennium Hotel in downtown Auckland.
The 63-year-old had arrived from Samoa on Christmas Day and had been carrying out his 14-day managed isolation when he died of natural causes.
His death was referred to the coroner.
Leiloa gained his qualification at Malua Theological College. He is survived by his wife, brother, three sisters and a large extended family.
Hundreds of people posted messages of support for the family on Bakulich's Facebook page.
One person described him as a "jovial soul and character always remembered". Another said they would miss "his encouraging messages and sense of humour".
To date, 106,195 people have gone through managed isolation and quarantine facilities across New Zealand since March 26 last year.
There are currently 5584 people currently housed in 32 hotels-turned-government-facilities in Auckland, Hamilton, Rotorua, Wellington and Christchurch.