New Zealand Football (NZF) is reported to have contacted the Peruvian Ministry of Defence after a military jet flyover above their team's hotel the day before a crucial match.
Peru coach Ricardo Gareca toasted an emotional victory on Thursday as he led the country to the World Cup for the first time in 36 years, with a 2-0 play-off second-leg victory against the All Whites in Lima.
But it came just a day after a jet flyover at 'remarkably low levels', not far above the All Whites squad's rooms on the 15th and 16th floor of a Marriott hotel, according to the New Zealand Herald.
The Peruvian Ministry of Defence is reported to have been contacted to ask how the flights had been allowed and to ensure there would be no repeat incident, after NZF sent messages to Wellington and the country's ambassador to Peru was made aware.
The move was interpreted as a show of 'unnecessary aggression' that must have been planned well in advance.
NZF CEO Andy Martin said:
"The fact that it was clearly a sanctioned action, that is clearly a step too far. We expected some disruptions and hassles here - that's how it is - but when the military get involved that is another level."
"It wasn't just the team, it was the rest of the Kiwis that were here.
"It was worrying. If that sort of involvement had taken place - which clearly had to be sanctioned for those sort of planes to fly - we wanted to make sure we had assurances for the safety of all of the Kiwis here, and in particular getting to the ground."
"We were protected, to a degree, but there were Kiwis fans out there just walking to the ground and we wanted to make sure they were going to be okay."
Local Peruvians who filmed the video were heard to comment "I can't believe it - what is this!" and "It's their hotel - what are they doing?"
The incident was one of a number of disruptions during the All Whites' trip.
Their plane's arrival in Lima was delayed by nearly three hours after Peruvian airport authorities cancelled their original flight plan.
Fireworks were also set off outside the team hotel in the early hours of the matchday morning - although this is said to have been expected and anticipated, to a degree.
Peru fans were also accused on social media of attempting to distract New Zealand, after lasers were pointed at players during the game.
On the field, Jefferson Farfan sent the capacity 40,000 home crowd at the Estadio Nacional De Lima wild with a 27th-minute opener, before Christian Ramos added another in the second half.
Peru's president Pedro Pablo Kuczynski tweeted:
"We waited more than 35 years to be in a World Cup again. Thank you, warriors, for giving us this joy."
New Zealand had their chances, especially in the second half after Burnley striker Chris Wood was brought on, but could not reach the finals for the first time since 2010.
Manager Anthony Hudson was proud of the efforts of his squad, though. He said:
"I'm proud of the team. Everyone should be proud of these players because what they've done is incredible."