Christian Brueckner, 45, is serving a seven-year sentence for raping an elderly woman at her home in Praia da Luz, and is currently being held at the Oldenburg correctional facility near Bremen.
In a letter to the Ministry of Justice, the prisoner claims he's had to stay in his cell for 23 hours a day after being threatened by other inmates.
"In the beginning, the fellow prisoners held back because they knew who I was, but had too little information about it," he wrote.
However, after a German documentary aired presenting further evidence from witnesses linking Brueckner to the disappearance of McCann, he said he's experienced 'insults and death threats'.
"I am forcibly self-isolating, since there is a high probability of a physical attack by fellow inmates," he wrote.
According to German publication Der Spiegel, Brueckner - who denies any involvement in the McCann case - said the confinement in his eight-square-metre cell is like 'torture'.
He also spoke about avoiding work at the prison factory over fears he may be attacked.
The prisoner continued: "Should any of the inmates, due to ignorance or for whatever reason, think that they want to seriously injure me physically or even kill me, the locksmith's shop is the ideal place for this.
"Tools are lying around everywhere and it is possible a sharp blade can be found in a few seconds.
"The repellent behaviour of the prisoners working there was so threatening for me that I asked for the termination of my employment."
Brueckner spoke out for the first time last year, writing another letter branding the accusations against him 'scandalous'.
He says the German legal system has made statements against him without ever charging him in connection with the disappearance of the child.
McCann went missing from her apartment in 2007 while on holiday in Portugal, days before her fourth birthday.
Her parents Kate and Gerry had gone out for tapas with friends while Madeleine and her siblings were in bed. When they got back, she had disappeared, and was never seen again.
Brueckner's letter, which was received by German tabloid Bild, said: "Charging an accused is one thing.
"Something completely different - namely, it is an unbelievable scandal - when a public prosecutor starts a public campaign for prejudice before a court case is opened.
"Freedom of expression is not a basic right so that everyone can say and write what they want. Freedom of expression does not protect the majority.
"It protects the minority. It does not protect the most logical, most convincing or most popular views, but rather the outsider position.
"I call on the Brunswick public prosecutors (Hans Christian) Wolters and (Ute) Lindemann to resign from their offices.
"Both are proving worldwide through my arbitrary condemnation in the past and through their scandalous pre-denial campaign in the present against me as an innocent person that they are not suitable for an office as a lawyer for the honest and trusting German people and you bring shame onto the judiciary."Featured Image Credit: Alamy/BBC News/YouTube