One of Egypt's most prominent revolutionaries has been taken into custody by the country's military rulers, provoking the biggest crisis yet in relations between pro-change activists and the increasingly repressive army junta.

Alaa Abd El Fattah, a 29-year-old who has been at the forefront of anti-regime struggles for a decade and was a political prisoner during the Mubarak era, was arrested on Sunday on charges of inciting violence against the military. He refused to recognise the legitimacy of his interrogators or answer their questions and is set to be held for 15 days, a period that can be renewed indefinitely by the authorities.

Presidential candidate Abdel Moneim Aboul Fotouh condemned the detention as "a major setback for the Egyptian revolution", while a number of campaign groups – including the influential 6 April movement – immediately declared a policy of total non-co-operation with army prosecutors, putting them on a guaranteed collision course with the ruling generals.

"Abd El Fattah's targeting is only the latest example of the systematic targeting of journalists, media figures, bloggers and activists by SCAF [the Supreme Council of the Armed Forces]," said the 'No to Military Trials' group in a statement. "As of today we refuse to co-operate with the military prosecution of civilians and we call on all Egyptian citizens to stand with us … This is not the new Egypt we have fought and died for."

Abd El Fattah comes from one of the country's most famous leftist families, the members of which have been a thorn in the side of Cairo's ruling elite for several generations. Part of Egypt's first wave of political bloggers, he and his wife Manal – who is expecting the couple's first child imminently – helped pioneer an online space in which opponents of the Mubarak dictatorship could organise and challenge the regime.

Since the toppling of Mubarak in February, Abd El Fattah had, like many other revolutionaries, turned his attention to the junta, whose early promises to defend Egypt's revolution and help move the country towards democratic civilian rule have appeared increasingly hollow with each passing month.

Following a night of bloodshed on 9 October when violence erupted at a Coptic Christian protest in central Cairo, Abd El Fattah was among those who spoke out against the army's involvement in the violence, which was confirmed by multiple witness reports and video footage.

He was subsequently summoned to Cairo's notorious C28, headquarters of the military prosecutors. More than 12,000 civilians are believed to have been sent to military trial since the army took power; human rights groups have condemned the tribunals as a gross distortion of legal justice.

"They [the army] committed a massacre, a horrible crime, and now they are working on framing someone else for it," said Abd El Fattah en route to C28 on Sunday. "This whole situation is distorted. Instead of launching a proper investigation, they are sending activists to trial for saying the plain truth and that is that the army committed a crime in cold blood."

Along with Abd El Fattah, more than two dozen other protesters have been accused by the military of inciting violence on 9 October – including one, Mina Daniel, who was killed on the night. One anti-revolutionary who goes by the pseudonym of Ahmed Spider claimed online that he submitted a complaint about Abd El Fattah to military prosecutors after witnessing video footage of Abd El Fattah throwing rocks, but no evidence has been supplied to support this.

Solidarity rallies for Abd El Fattah have been called in Cairo, Alexandria and Tunisia, where revolutionaries are planning a mass demonstration outside the Egyptian embassy.