He said their investigation began after Customs received a tip-off from international sources about the man's involvement in sharing child sexual abuse images on a popular social media messaging app.
A search warrant was carried out at his home last week, where further evidence was found resulting in his arrest.
In the second and separate case, the 26-year-old was arrested in Auckland last week, after a forensic search of his mobile phone located images and video of children being sexually abused.
The man, who lives overseas, first came to Customs' attention in 2015, after an international referral for similar offending overseas. When he recently returned to New Zealand for a short holiday, Customs officers questioned and searched the man.
Waugh said every time child sexual abuse images or videos were downloaded, uploaded or shared online, it contributed to the further victimisation of the children.
"This is also true if the objectionable material is taken across the border, when travelling.
"There is an entire global network dedicated to combating the unacceptable crime of child exploitation. Here in New Zealand, Customs works closely with the NZ Police and Internal Affairs to safeguard and rescue victims, while holding the perpetrators to account."