New Zealand take on Oman in an international friendly in Muscat on Friday and the report claims that the message used to inform players of their selection was sent to the group that drew with Myanmar in September.
All Whites team management use messaging app WhatsApp to communicate logistical details with their network of players around the world.
Seven players from the Myanmar match were not picked to travel to the Middle East and one player told 3News that he only discovered he had been dropped after he had been removed from the WhatsApp group.
A NZF statement said team management "followed its regular official internal squad announcement process to the selected players".
"As usual, all members of the wider squad of more than 40 players were aware of the date on which they would receive notification if they were selected for this tour," the statement added.
This is the latest in a series of incidents which have damaged the sport's governing body's credibility.
It was rocked by an eligibility drama which saw the national under-23 side disqualified from the Olympics qualifying tournament, while questions are being asked over its support of the Phoenix in their battle to stay in the A-League.
The All Whites have also slumped to a record low world ranking of 148 and head to Oman having not won a game in more than two years.