In his evidence earlier this week, Mr Whitehead said he discovered 12 of his hives located along Horeke Rd were missing during a check on March 23, 2015.
No one had permission to take them, he said.
He has been a beekeeper for 30 years and said he has thousands of hives between Whangarei and Taipa.
Howes also pleaded guilty to one charge of falsifying an apiarist in breach of the Animal Products' Act.
He used an apiarist's name to commercially extract just under 2000kg of honey at Marshwood Apiaries in Kaiwaka in April 2015.
During his sentencing in July, the Crown will withdraw two charges of theft and another two of obtaining by deception.
They relate to an allegation that between June and October 2015, Howes stole two 6m containers that had beehives, boxes, bases, frames and other beekeeping equipment.
The items, worth $46,000, belonged to NZ Queen Bee.
In September 2015, Howes allegedly stole a 6m shipping container valued at $2645, also belonging to NZ Queen Bee.
Howes was remanded on bail to reappear for sentencing on July 12.