The men, aged 22 and 25, will appear in Tauranga District Court on Friday.
Police were still trying to find the other man who was in the boat at the time of the capsize, Liam Kane, 22.
He has not been seen since raising the alarm with a member of the public last night.
Inspector Karl Wright-St Clair said Mr Kane appeared to be in good health but police wanted to talk to him about what had happened.
"It could be that he has information about events that would assist those coordinating the search and help bring some answers to Shaun's family, who are understandably very distressed.''
Police said none of the men were experienced on the water and the weather conditions were poor.
The aluminium dinghy was discovered at Matakana Island this morning by members of the Mt Maunganui Surf Club, as they searched the waterways in an inflatable rescue boat.
The dinghy was upside-down near the base of cliffs between Matakana Point and Tahunamanu Point, directly north of Omokoroa Point, where the men set off from last night.
It appeared to have been pushed towards Matakana Island by the wind and current.
Police planned to examine the boat today.
Mr Hogarth's family released a short statement this afternoon.
"We're all together as a family and are hoping and praying that he's safe somewhere and will be found soon.''
