"On the evening of October the 12th, 2016, Jaber Albakr, the prime suspect in planning a serious attack against the state, took his life in the prison hospital of the Leipzig correctional facility," the ministry said in a statement on its website, also confirming the news to CNN.
The Saxony Justice Minister Sebastian Gemkow told reporters that Albakr had strangled himself with his shirt but it was not immediately clear if he had hanged himself in his cell.
Gemkow said Albakr had been seen by a psychologist earlier in the day, but it was assessed that suicide was unlikely.
Authorities then decided to reduce its checks on him from every 30 minutes to every 15.
Albakr was on a hunger strike and refused to drink, Gemkow said, adding that authorities tried to resuscitate him for about half an hour after they found his body.
There was no video surveillance of his cell in accordance with local law, Gemkow explained.
Germany's Spiegel Online had earlier reported that Albakr had been under round-the-clock surveillance in police custody and was considered at risk of suicide.
Arrest attempt questioned
Albakr was arrested overnight Sunday after two Syrians tied the suspect to a sofa in their flat in Leipzig and alerted police. Crime office officials said that Albakr had befriended them at a train station in Leipzig and had asked to stay with them.
His hosts learned from social media that Albakr was wanted by authorities and contacted police to come to their apartment and detain him.
Albakr's capture ended a manhunt that lasted almost two days, and the manner of his arrest has raised questions about whether police botched an attempt on Saturday to detain him. CNN was not able to immediately contact the police Thursday. The Saxony justice ministry is expected to give a press conference later Thursday.
In a raid on an apartment in the city of Chemnitz on Saturday , which appeared to be Albakr's home, police discovered a mix of explosives weighing 1.5 kg that they described as more dangerous than TNT. The German prosecutor's office said the mix could cause significant damage in small amounts.
Police carried out a controlled explosion to gain access to the apartment.
Among the materials found was what police suspected to be TATP, or acetone peroxide, which was used in recent terror attacks in Brussels and Paris, Saxony's crime office said.
Markus Ulbig, Saxony state's interior minister, said that Albakr had come to Germany as an asylum-seeker in February 2015. A year later, he formally asked for asylum, which was granted in June this year.
German Chancellor Merkel has come under intense political pressure for her open-door policy on refugees. German officials said the country welcomed more than 1 million refugees in 2015 alone, many of them Syrians fleeing the war in their country.
There have been several low-impact attacks in Germany this year carried out by refugees, prompting Merkel's administration to tighten security measures.