Brazil's navy said in a statement issued Saturday that the 43-year-old was between the cities of Codajas and Coari when she activated an emergency beacon on September 13.
Ms Kelty disappeared in the upper stretches of the Amazon in northern Brazil often referred to as the Solimoes river - an area known for pirate attacks and drug traffickers.
"The information that we have is that her objective was to follow the Amazon river all the way to its mouth", said Paulo Veiga, the captain of the District Naval Command in Manaus.
Before setting off on the river trek, Emma wrote on her website of her fears of "notorious drug barons" and "organ harvesting folks" along the route.
A 17-year-old man has been arrested in connection with the murder of a British adventurer in Brazil. "His body has never been found", says the Telegraph.
One of them told police Ms Kelty was camped on Boiero Island when two people approached her. She was shot twice with a 20-gauge sawn-off shotgun and dumped in the river. Her body was then thrown into the river.
According to the teenager, whom police did not name for legal reasons, the group tried to sell her two mobile phones, her tablet computer and her GoPro camera in local communities.
Coari chief detective Jose Afonso Barradas Junior said the region was problematic for pirates who committed robberies and there were drugs coming from Colombia.
The self-confessed adrenaline junkie had only begun serious kayaking earlier this year - just weeks after skiing a return solo journey to the South Pole.
A statement from Ms Kelty's family said they were extremely proud of her and her "strength would be sorely missed".
Olie Hunter Smart, an explorer who completed a similar route in 2015, said Coari was known to be a risky area.
Mr Smart, who is now walking the length of India, said: "The Emma that I met was an incredibly fearless and courageous person who lived life to the full".
The investigation into her death continues.