Fears for Egypt's democracy deepened on Monday when a judge sentenced 683 men to death in the country's latest mass trial, while another banned a youth movement that helped inspire Egypt's 2011 revolution.

The 683 men – including the Muslim Brotherhood leader, Mohamed Badie – were condemned to death in the southern city of Minya on charges of killing a policeman last August.

In a similar but separate case, the same judge then upheld the death sentences of 37 of 529 men he notoriously ordered to hang last month, bringing the total number of death sentences to 720. The remaining 492 had their sentences commuted to 25-year jail terms. All cases are subject to further appeals.

Lawyers and rights campaigners said the sentences in the two mass trials resulted from rushed proceedings that infringed basic local and international law.

Mohamed Elmessiry, an Amnesty International researcher who attended the hearings, said: "In each trial, the defence were not able to present their case, the witnesses were not heard, and many of the accused were not brought to the courtroom. This lacks any basic guarantees of a fair trial – not only under international law, but also Egyptian national law.

"The trials themselves are a death sentence to any remaining credibility and independence of Egypt's criminal justice system."

Amnesty has previously said the 529 case was the largest batch of simultaneous death sentences in the world in living memory – a record now beaten by Monday's developments.

Both cases form the latest instalment of a government crackdown in which at least 16,000 people have been arrested and more than 2,500 killed since the removal of the Muslim Brotherhood's Mohamed Morsi as president last July.

A spokesman for the 6 April youth group, Ahmad Abd Allah, said the banning of the group highlighted the extent of Egypt's counter-revolution.

"It shows that it's not just the Islamists who are being targeted, it's also liberal groups like us. And [the government] will continue all the way to close down all democratic forces," Abd Allah said. "And it's just the beginning."

Prosecutors said the defendants in both court cases were Brotherhood members who collectively killed two police officers during an explosion of nationwide violence last August. The 529 defendants were found guilty of lynching a policeman in Matay, in Minya province. On the same day, the 683 others are said to have killed an officer in the nearby town of Adwa.

But many of the defendants in both trials say they were not present during the attacks, and some say they are not even supporters of the Brotherhood but were reported to the police by informants acting on personal agendas.

"There is nothing against me – no one has any evidence that I was there on that day," said Hagag Saber, a 34-year-old government electrician who was one of the 683 sentenced to death for the Adwa killing. Currently at large, he claims he was in Cairo the day the attacks happened.

"There is no justice or integrity, nothing based on facts. Everything is based on an illegitimate investigation that took hearsay from people in the street," Saber said.

His lawyer, Mohamed Abd-El Fatah Ali, showed the Guardian roughly 6,000 pages of court documents from the case and argued that the judge could not have had time to read them.

"There's no human who could read this amount of newspaper pages, let alone legal documents containing testimonies, in order to find the paragraph that relates to this case and these defendants in the time allowed," said Ali, who was fined by the judge and referred to court himself for boycotting an earlier session. "That would take three months."

Families alleged that some defendants were not even mentioned in the documents. One of Ali's lawyer colleagues, Ahmed Eid, was arrested because of personal differences with policemen, his family claimed. Previously a defence lawyer in the 529 case, Eid joined his clients in jail after the case had officially been referred to court.

His wife said police arrested Eid because he had failed to pay them a bribe, and that investigators – with whom he was in daily contact on behalf of his clients – had never previously suggested he was involved in the case.

Eid, a supporter of the former dictator Hosni Mubarak, is one of several men who say they are unaffiliated with the Brotherhood but are among those sentenced. Another is the cleric Ahmed Korany – despite his family providing written testimony to the court from witnesses who said he was not involved in the crimes.

Korany's lawyer, Ahmed Shabib, said: "It's very well known that he was against the Brotherhood, so I was so surprised to see him among the defendants."

In passing the sentences, the judge, Saeed Youssef, ignored an international campaign in which more than 1.5 million people signed a petition hosted by the online activists Avaaz calling for a re-trial.

But in Egypt the outcry has not been universal. Many saw the 529 death sentences as a fitting revenge on the Brotherhood, who are blamed for a wave of militancy across Egypt in recent months. "The outrage over the conviction of 529 terrorists is in itself an outrage," summarised one commentator in a state-run newspaper this month.

After the 529's initial sentences in March, Egypt's foreign ministry released a statement defending the court's integrity. "The sentence was issued by an independent court after careful study of the case," the statement read.

The 683 death sentences will now be referred to Egypt's Grand Mufti, a senior Muslim cleric, for his opinion. The 529 from the second case will be referred to an appeal court, since the mufti has already been consulted on their sentences. In an odd aside, the judge recommended that the prosecution seek the reinstatement of the death penalty for the 492 whose sentences were commuted.

Judicial experts said the case was unlikely to have been expressly ordered by a central figure, such as Egypt's influential army chief, Abdel Fatah al-Sisi. Nathan Brown, a professor at George Washington University, and an expert on the Egyptian judiciary, told the Guardian last month: "I think it is more a matter of a common mentality than direct co-ordination. Indeed, the court here has gone so far that it is difficult to see that it serves the interest of the regime."