UPDATED 5.01pm: Counties Manukau Police have confirmed it's investigating after a man was found dead while in police custody this morning.

The 64-year-old was arrested on Monday night and was alone in custody throughout the night.

He was routinely checked throughout the night until his discovery at 5.40am.

The cause of death has yet to be established and is awaiting the results of a post mortem examination.

"This incident is a tragedy and we extend our deepest sympathies to his family," said Police District Commander Superintendent John Tims.

"We are doing everything we can to support the family at this difficult time." 

The incident has been referred to the IPCA.