In February 2007 Mammadov was arrested on charges of cooperation with Iranian intelligence. The charge was based on the claims of Elman Guliyev, employee of the Talysh Cultural Centre, who was charged with him, and who pleaded guilty. According to the investigations, Mammadov had received $1,000-2,000 from Iranian authorities for publishing his newspaper. The paper is published in Talysh language in Baku.

On June 24 the same year, the grave crimes court found the two guilty on count 274 (high treason) and sentenced Mammadov to 10 and Guliyev to 6 years of imprisonment. In response to the verdict, Mammadov claimed his charge was ethnically motivated. Human rights activists called Novruzali Mammadov a political prisoner and further described the charges against him as groundless.
 
On 18 January 2009 Mammadov was put in “solitary confinement” in Prison #15. As a result he developed serious health problems, and appealed to court for medical attention. In March, the court issued a decision to immediately transfer him to a hospital. However, the prison leadership ignored the court’s decision. Mammadov was kept imprisoned, and his health deteriorated further. When Mammadov’s condition turned critical on 28 July, he was transferred to the Justice Ministry’s Penitentiary Services Central Hospital. It was there that he died on 17 August. The elderly scientist suffered from cardiac insufficiency, hypertension and many other diseases and was buried in his native village Arkivan in Astara region on 18 August.

Considering the seriousness of Mammadov’s health problems, local and international organizations (Council of Europe Secretary General’s Special Envoy for Azerbaijan Veronica Kotek, Ombudsman Elmira Suleymanova and others) called for the editor to be placed in a civil hospital, and to invite a medical expert via the Council of Europe to see him. Andres Herkel, rapporteur of PACE Monitoring Committee, visited Mammadov in jail in April, and his relatives kept insisting on him being treated in a civil hospital. Despite the hospital’s admission that Mammadov’s condition was serious and deteriorating, this was not permitted.

While Azeri authorities claim that Mammadov’s guilt of espionage and high treason has been proven, the Azerbaijan Federation of Human Rights Organizations explicitly declared him a political prisoner, alongside 65 others currently serving sentences in Azeri prisons. On these grounds, domestic and international human rights organizations repeatedly requested the Azerbaijani officials to free Mammadov. Now, Mammadov’s death will instead be the subject of strong criticism from the international community.