The birds had injuries consistent with dog attacks and DNA tests showed saliva from the same dog on both.
After further reports that Allen's dog had been wandering, it was seized by a council animal control officer on July 24. Its DNA was a perfect match for the saliva found on the dead kiwi.
Allen told the court Weka was not his dog, but one he had inherited from a previous relationship. It had been left on the deck during the day, but could not escape because the deck was 3.5m above the ground.
Because the only exit from the deck was via his home, Allen said, someone must have entered his house on each occasion while he was at work and let the dog out.
Judge Orchard said the dog's wandering suggested it should have been kept in a proper kennel and run rather than left unsecured on the deck. She also noted that at the time of the kiwi deaths Allen was effectively already on notice to control the dog after the council issued two fines for allowing it to attack stock.
''This points to him having a very cavalier approach to his responsibilities. The dog got out on multiple occasions, and was clearly able to roam freely, including at least once at night," she said.
Allen, who along with others needed to be deterred from further offending, was fined $4500, after a "merciful" $500 discount for his guilty plea, which was entered on the day of his trial, two years after charges were laid.
Allen made no application to stop the dog's destruction, and DOC made no application for reparation for the costs of DNA testing.
The council's seizure of a previous husky owned by Allen and his then partner Lisa Wynyard, Laska, sparked a public outcry in 2017. In that case the dog was accused of attacking protected weka while roaming off their property.
The couple maintained Laska had been wrongly accused, and fought a long battle to have her released. A newspaper ran a series of front-page stories and a 'Help Save Laska' online petition attracted 29,935 signatures, of which 27,377 were from overseas.
In the end Laska was rehomed with a Waikato family.
Allen was originally charged with two counts of owning an animal that killed protected wildlife but that was reduced last week to one representative charge. The maximum penalty was three years' jail or a fine of $20,000.