The body was exhumed in 2010 in a bid to confirm the cause of his death.
Brahe was thought to have died of a bladder infection, but a previous exhumation found traces of mercury in hair from his beard.
However, the most recent tests have found the levels of mercury were not high enough to have killed him.
Some have speculated that he was killed on the orders of the Danish king, or by fellow astronomer Johannes Kepler, who also later gained fame.
A team of Danish and Czech scientists have been working to solve the mystery by analysing bone, hair and clothing samples.
"There was mercury in the beard, you will also have traces of mercury if you have a beard... But the amount of mercury was as you see in people [alive today]," Dr Jens Vellev, from Aarhus University in Denmark, who is leading the investigations, told BBC News.
Dr Vellev now thinks there was no foul play involved in Brahe's death.
"It is impossible that Tycho Brahe could have been murdered," he explained. When asked whether other poisons could have been used, Dr Vellev said: "If there were other poisons in the beard, we would have been able to see it in the analyses."
Instead, he says, the description given by Kepler of Brahe's death at the age of 54 matches up well with the progression of a severe bladder infection.
One widely told story about Brahe was that his bladder burst at a royal banquet when he had been too polite to leave the table and relieve himself. Accounts say he died 11 days later.
Tycho was born Tyge Ottesen Brahe in 1546 in Scania, which at the time was a Danish province, and studied astronomy at the University of Copenhagen, as well as German academic institutions.
He catalogued more than 1,000 new stars and his stellar and planetary observations helped lay the foundations of early modern astronomy.
On his death in 1601, the astronomer was buried at Tyn Church near Prague's Old Town Square.
His body has been exhumed before, in 1901. Tests on a sample of hair from his moustache, taken at that time, have been conducted as recently as the 1990s and indicated the presence of mercury.
Brahe's fame is also partly due to his personal life.
He lost the bridge of his nose in a duel while at the University of Rostock in 1566, and wore a metal prosthetic for the rest of his life.
Dr Vellev said tests now indicated that the prosthetic was in fact made of brass, not gold and silver as accounts had suggested.
The 16th-Century Danish astronomer Tycho Brahe is unlikely to have been poisoned, according to a researcher studying his remains.