An Auckland Airport spokeswoman said passengers and staff were evacuated from the hall immediately and have since been allowed back in.
Gary Flood-Smith said after he and his wife landed on their flight NZ281 from Singapore about 10pm they were kept in the Customs area about an hour and a half.
"I asked [Customs officials] what was going on but they didn't say anything."
Flood-Smith only discovered two shells had been found when he got home and read the Herald online.
"My concern is that they didn't evacuate us, but it was deemed dangerous enough for them to evacuate the rest of the airport.
"I understand these things happen, and they can't just let people through Customs, but you don't know how dangerous these things are.
"They should have things in place for when something like this happened, like another secure area they could take us all to."
He said he didn't think the shells were on his plane as there were already operations under way when they landed.
Twitter user Jamie Goode said he arrived into Auckland on a 787 Dreamliner and was faced with a two-hour wait because immigration was closed.
