Argentine forensic scientists said they found no DNA from the students at a rubbish dump outside the town of Cocula.
The government says the students were killed there.
It said their bodies were burnt, after police handed them over to a gang.
But after a year-long investigation the Argentine Forensic Anthropology Team concluded there was no biological or physical evidence to show that the 43 students who disappeared in 2014 were burnt and killed at the rubbish dump.
The team said they had evidence that there had been a number of fires over the years at the rubbish dump in a canyon outside Cocula but none had been big enough to burn 43 bodies.
They said they found bone fragments from 19 people but none came from the students.
The government had said that the students were arrested on 26 September 2014 in the town of Iguala around 20 km (12 miles) away by municipal police.
The Prosecutor General at the time, Jesus Murillo Karam, said that his investigations had uncovered that the police had handed over the students to a drug trafficking gang who had killed them at the rubbish dump and then built a large funeral pyre with the bodies to burn them.
The gang allegedly collected up the ashes and remains after the fire in bags and threw them into a nearby stream.
The government has said it has identified the remains of two of the students from the bags, Alexander Mora and Jhosivani Guerrero, although only the first could by fully identified through DNA sampling.
The Argentine team said it had not been present when the bags were found so could not be sure of the remains' origins.
It said the bones that had been analysed by an Austrian laboratory to identify Alexander Mora, were "unusual in size compared to the other fragments in the same bag".
It has also had minimal exposure to fire, the group said, and there was "not any sign of a recent fire in the vegetation" at the rubbish dump.
In September, experts from the Inter-American Commission on Human Rights concluded the government's original investigation had been deeply flawed.
In response to the new report, the Mexican Attorney General's office said the case of the 43 students was not closed and that the authorities were finalising a team to conduct a new analysis of the fire claims as well as looking at new lines of investigation into what had happened to the students.
The parents of the students have been campaigning to be given access to military barracks in the area which, they say, may contain clues about the whereabouts of their children.
The government has refused to let the soldiers who were in the area at the time of the disappearance be questioned by anyone but government prosecutors.

Propper has signed a four-year contract with the club, which was promoted to the Premier League last season.
Brighton boss Chris Hughton said the 25-year-old, who has five caps for the Netherlands, is "a strong competitor".
The fee tops the £5m which the club are thought to have paid Valencia in June for Australia goalkeeper Mathew Ryan.
Propper scored 16 goals in 67 league appearances after joining PSV from Vitesse Arnhem in 2015 and helped the club win the league title in his first full season.
"There is no doubting his pedigree, Davy has played a number of matches in the Champions League for PSV, as well as international football for the Netherlands," added Hughton.
"He will complement our existing midfield players, and he is also a really good age."
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The 48-year-old retired in 2005 after an illustrious career, scoring 168 goals for the Italian club and 56 times for his country.
But he told Fifa.com he has "difficulty walking" because of the effort he put into his game.
"I gave much more than I actually had to give," Batistuta said.
In 2014, Batistuta revealed he had asked doctors to amputate his legs because of the severe pain he was suffering.
After surgery to relieve the pressure on his cartilage and tendons, his condition improved, but he has been left with mobility problems.
A second report into the disappearance of 43 students in the southern Mexican state of Guerrero says there is no evidence to support the official version of what happened to them.
[NEXT_CONCEPT]
Brighton have broken their transfer record to sign Dutch midfielder Davy Propper from PSV Eindhoven in a reported £6m deal.
[NEXT_CONCEPT]
Former Argentina and Fiorentina striker Gabriel Batistuta has revealed he struggles to walk after his 17 years in football.