The Honduran National Football Federation on Monday posted on Twitter footage of a drone flying above Sydney's Olympic Stadium where the team trained after their long flight from Central America.
Honduras face the Socceroos at the same stadium on Wednesday in the deciding second leg of their intercontinental playoff with the scores level at 0-0 after a tight first leg in San Pedro Sula on Friday.
While Football Federation Australia said they were not involved in the drone incident, Pinto said the affair was "embarrassing for such an advanced country".
"Let's not be innocent, it's espionage in football," he told reporters through a translator on Tuesday.
"When Australia went to Honduras, they checked every bathroom, every box at the stadium where they trained.
"It just takes some of the merit away from the fair play and the sporting event that will be held tomorrow."
Pinto was also involved in a row with the media at the start of Monday's session when he tried to close training before the 15 minutes of open access allowed under FIFA rules.
The Colombian also suggested on his arrival in Sydney that someone in the Honduran media had leaked tactical details to Australia.
"Regardless of the incident with the drone, and the possibility of a journalist from Honduras leaking information regarding our team, we are happy with the welcome we have had here," said Pinto.
"We are facing a balanced side. We need to be aggressive and I'll be even happier we're able to go back to Honduras with qualification."
Honduras's bid for a fourth appearance at the World Cup finals, and third in a row, has been far from plain sailing and they needed two second-half goals to clinch a place in the playoff with a 3-2 win over Mexico last month.
On Wednesday, Pinto will be able to call on experienced captain Maynor Figueroa and winger Alberth Elis, who were both suspended for the first leg.
But it is the long balls through to forward Carlo Costly, who came close to breaking the deadlock in the first leg, that might concern Australia most as they seek to avoid conceding an away goal.
"Without a doubt we'll be employing long balls tomorrow," Pinto said.
"If the head coach of Australia is watching the press conference, he has an insight into our gameplan."
(Additional reporting by Andrew Downie in Sao Paulo, editing by Ian Ransom/Peter Rutherford)
