"We do a serious job with those isolated Indians and this is not a joke," he said.
The photographs, showing red-painted tribes people aiming spears and arrows at an aircraft flying over their jungle home, grabbed attention around the world.
|Meirelles said he had known of the tribe's existence for 20 years [Meirelles Family]
The Observer said the decision to fly over the tribe and capture the images was a form of contact in itself that would raise "awkward questions".
Meirelles, a 'sertanista' – a person who scours the Brazilian Amazon jungle in search of isolated tribes - also said that while there had been "tales and stories" about the existence of the tribe since 1910, it had remained "uncontacted".
"Our policy at FUNAI (the Brazilian government agency responsible for the Indians) is not to make contact - it is to preserve their territory without contact," Meirelles said.
He said that after the unexpected and unique photos of the Indians were taken, during a routine flight over the area, the decision to release them to the media was a calculated one.
He said his team released the images as a way to attract media attention to the threats to the tribe's existence, especially from illegal logging in Peru that encroaches into the Brazilian Amazon state of Acre.
"Yes, those pictures were released to the media for a reason; to alert the world about the existence of that tribe so nobody can say they don't exist," Meirelles said.
Survival International, an organisation that campaigns to protect isolated tribes, also rejected claims made in the Observer article.
"The Observer article claims to 'reveal' that the tribe photographed was neither 'lost' nor 'unknown'. The reality is that neither Survival nor the Brazilian government claimed they were," Stephen Corry, of Survival International said.
Meirelles said he worked to create an area around the tribe to protect them, "so of course we know that some uncontacted tribes existed there – that is our job."
"Those Indians have been known to me, generally, for 20 years. Myself or FUNAI have never said otherwise.
"We know of the existence of the isolated Indians in that area, but we make no physical contact with them," he said.
Meirelles told Al Jazeera in an exclusive interview earlier this month that Brazil has 69 references to isolated tribes with little to no contact with the outside world – 22 of which have been confirmed, several by Meirelles himself.
Many of the tribes live in the remote jungles on the border between Brazil and Peru.