"We wish to extend our sympathies to this person's family during this stressful time," said the spokesperson.
In a release about the death, the ministry said it wished to acknowledge the efforts of the managed isolation facility's staff and paramedics.
A police media spokesperson said police attended the Crowne Plaza in relation to a sudden death.
The death appeared to be a medical event.
The latest death comes just days after the Ministry of Health launched a review into the home isolation system as a result of two people dying while isolating at home with Covid last week.
A man in his 50s died in his Mt Eden home on Friday and another died at a Manukau apartment on Tuesday. Both deaths have been referred to the Coroner.
In August, the Crowne Plaza was the focus of the source of the Delta outbreak that plunged the country back into lockdown because of genomic sequencing results matching a case who travelled from Sydney, arriving in Auckland on August 7.
The hotel was temporarily closed to guests while the Auckland Regional Public Health Service investigated a link between a returnee who tested positive for Covid-19 and a public walkway that was potentially the source of the current Auckland outbreak.
However, an additional assurance review confirmed that the procedures and ventilation at the facility met the relevant standards and it was re-opened to guests arriving from overseas on September 8.
