Mr Napier said the fire came at a time when the company, which first introduced barn eggs in New Zealand, was preparing an inaugural export to Singapore.
The contract was a breakthrough for Henergy Eggs in a market favouring barn eggs as less of a food safety risk than free range eggs.
The first shipment was due for consignment a week ago but there had been a "logistics delay" with the supermarket changing its systems.
The Masterton eggs would now begin shipping to Singapore from September 11, he said.
"It's not a major export yet but it could become significant for us in the future. But we're fully operational and the fire has not affected that contract in any way - it's business as usual."
"We do need that storage space though and in the meantime we may hire temporary container storage as a stopgap until we put a new building there."
He said construction of a replacement building would easily cost "hundreds of thousands" and may not start until next year.
A farm manager had spotted smoke rising from the storage building and raised the alarm on Monday, and Mr Napier had at first feared for the safety of his staff and the nearby poultry and buildings.
A "fortunate" southeasterly wind and the efforts of firefighters dampening the hens' buildings and the pack house had kept the blaze from becoming far worse, he said.
"The building was full of packaging - moulded fibre egg cartons - and that really is major fuel once it's alight. There was a lot of heat, a lot, going on to all the surrounding buildings but the wind was blowing the right way."