They travelled the length of the loch on research vessel Deepscan taking water samples from three different depths.
The scientists collected DNA left by creatures in the loch from their skin, scales, feathers, fur and faeces.
The DNA samples were then sent to labs in New Zealand, Australia, Denmark and France to be analysed for the final findings.
Professor Neil Gemmell of the University of Otago, New Zealand, who led the study, said the results are "surprising".
He says his team tested the data against most of the main theories about the Loch Ness Monster.
Professor Gemmell said that while the full details will be released at a later stage, one of the theories "might" be correct.
One theory is that the monster is a long-necked plesiosaur that somehow survived the period when dinosaurs became extinct, or it is a sturgeon or giant catfish.
Professor Gemmell said he hoped to announce the full findings of the study in Scotland next month - but would not confirm which hypothesis might be right.
The Loch Ness Monster
The Loch Ness Monster
This shadowy something is what someone says is a photo of the Loch Ness monster in Scotland. (AP PHOTO)
The Loch Ness Monster', 1933, (1938). A photograph purporting to show the Loch Ness Monster (Nessie). From These Tremendous Years 1919-1938. [Daily Express, London, 1938] Artist: Unknown. (Photo by The Print Collector/Getty Images)
FILE -This is an undated file photo of a shadowy shape that some people say is a photo of the Loch Ness monster in Scotland. For hundreds of years, visitors to Scotland's Loch Ness have described seeing a monster that some believe lives in the depths. Now the legend of "Nessie" may have no place to hide. Researchers will travel there next month to take samples of the murky waters and use DNA tests to determine what species live there. (AP Photo, File)
Gerald McSorley holds up a Jurassic fossil, clearly showing four prefectly preserved vertebrae, complete with spinal cord and blood vessels, which he found on the shores of Loch Ness, at his home in Stirling in Scotland, July 16, 2003. Though experts have stressed that the find is not related to the original Loch Ness monster - the remains of the plesiosaur (a long-necked, carnivorous sea reptile) are around 150 million years old and Loch Ness did not exist until the last Ice Age around 12,000 years ago - they say the find is evidence that the 35-foot-long creature once existed in the area.
DRUMNADROCHIT, SCOTLAND - APRIL 13: John Haig an engineer moves a Munin robot, operated by Norwegian company Kongsberg Maritime in Loch Ness on April 13, 2016 in Drumnadrochit, Scotland The Norwegian company Kongsberg, which has been surveying the loch came across remains of a thirty metre model of the Loch Ness Monster, from the 1970 film The Private Life of Sherlock Holmes, discovered down on the loch bed by the underwater robot. (Photo by Jeff J Mitchell/Getty Images)
Have a team of scientists discovered proof the Loch Ness Monster exists? (Picture: PA)
Loch Ness, Scotland, February 1989. Scientist Thayne Smith Lowrance using a Lowrance sonar device during an attempt to find the legendary Loch Ness Monster. (Photo by Tom Stoddart/Getty Images)
DRUMNADROCHIT, SCOTLAND - MARCH, 1987: The sun rises over Loch Ness in the Scottish Highlands near Drumnadrochit. The large freshwater loch is believed by some to be the home of the Loch Ness Monster. The ruins of the 13th century Urquhart Castle overlooks the loch. It is near this castle that the majority of Loch Ness Monster sightings have occured. (Photo by Robert Alexander/Archive Photos/Getty Images) 5104602RA_Scotland01.jpg
Frank Searle a photographer who studied the disputed existence of the Loch Ness Monster. He took up residence at Loch Ness in 1969 living a frugal existence in a tent then a caravan looking for definitive proof of the monster's existence. Eventually photographs began to appear from 1972 onwards and earned Frank a degree of fame as a monster hunter, 8th May 1975. (Photo by Staff/Mirrorpix/Getty Images)
The Goodies Trio are Tim Brooke-Taylor, Graeme Garden & Bill Oddie. (Photo by Daily Mirror/Mirrorpix/Mirrorpix via Getty Images)
7th July 1969: A submarine is lowered into Loch Ness to begin its search for the monster. References to a monster in Loch Ness date back to St Columba's biography of AD 565, where Adamnan describes St Columba preventing a creature in the Loch eating a Pict. More than 1,000 people claim to have seen 'Nessie' and the area is a popular tourist attraction. (Photo by Ian Tyas/Keystone Features/Getty Images)
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He said: "Is there anything deeply mysterious? It depends what you believe. Is there anything startling? There are a few things that are a bit surprising.
"What we'll have achieved is what we set out to do, which is document the biodiversity of Loch Ness in June 2018 in some level of detail.
"We've tested each one of the main monster hypotheses and three of them we can probably say aren't right and one of them might be."
Hundreds of thousands of visitors flock to Loch Ness every year to try and catch a glimpse of the mythical monster.
Nessie is worth millions of pounds to the Scottish economy - and tourist bosses previously said they are "eagerly anticipating" the results.
Announcing the study last year, Professor Gemmell said: "Scotland is dear to my heart because my mother and her family are Scottish, I'm delighted to be here to undertake our environmental DNA investigation of Loch Ness.
"It's a place of extraordinary natural beauty.
"We're delighted with the amount of interest the project has generated in the science and, monster or not, we are going to understand Loch Ness, and the life in it, in a new way."