The items, worth $46,000, belonged to NZ Queen Bee.
In September last year, Howes allegedly stole a 6m shipping container valued at $2645, also belonging to NZ Queen Bee.
Three other charges were laid earlier - breaching the Animal Products Act by falsifying an apiarist and beekeeper statement and two charges of theft of beehives.
Mr Kim said Howes' employment ended in August 2015 when Mr Kim went to move his hives but they were missing.
He said Howes did not respond to three emails he sent wanting to discuss the missing hives.
Mr Kim said he paid $8797 on January 11, 2015, for three shipping containers from a company Howes recommended.
The containers were to be used to store equipment at the back of NZ Queen Bee.
But Mr Kim said the containers were found at Howes' mother's house in Titoki.
Mr Kim said when he entered the property where he discovered the containers, Howes told him to leave.
Howes was not allowed to move the shipping containers without permission, Mr Kim said.
He later found 44 missing hives at multiple locations, including 20 at a Waipu Cove Rd site.
The trial continues before a judge.