The new Tunisian government is still holding between 500 and 1,000 prisoners accused of often vaguely worded terrorism offences, despite a promise to release all political detainees.

While hundreds of prisoners of conscience have already been released since the fall of the government of the dictator Zine al-Abidine Ben Ali last week, concern is mounting over the uncertain fate of a second group convicted under draconian anti-terror laws.

According to those familiar with their cases many were tried under deeply flawed legal procedures or had confessions tortured out of them, often after being targeted for their religious beliefs.

"There is a question that needs to be answered about who is a political prisoner," said Denis Robiliard, who was with an Amnesty International team in Tunisia when Ben Ali was deposed.

"Most of the prisoners of conscience – people who had been imprisoned for their views – have been released. But there is a second group of people: those who were convicted under the anti-terrorism legislation. How many there are is a matter of dispute but people talk about between 500 and 1,000.

"I think if they are not freed they must be retried with a fair trial because all of the trials were unfair with confessions extracted by torture and a lack of an independent judge. The first thing that is required is for the new government to produce a list of all those it is holding under its anti-terror laws."

Samir Ben Amor, a Tunis lawyer who has defended some of those charged under the anti-terror legislation, agrees hundreds are still being held. "Yes there are people who tried to commit [terrorist] acts against the regime," he said, "but there are dozens, not the thousands who were prosecuted.

"People say that all political prisoners have been freed but there are still people in prison who are being held under the anti-terror laws who have had confessions tortured out of them. Part of the problem is that the government did not recognise the term political prisoner."

He added ironically: "The old regime of Ben Ali used to say this is a safe country. There is no terrorism in Tunisia. But we have 'terrorists' in jail."

Despite the new government's repeated insistence that it has given a blanket amnesty to all political groups, including the banned Islamist opposition, protesters have complained that only a few hundred of those imprisoned for political reasons during Ben Ali's 23-year rule have been released.

Families gathered outside Borj Lamary prison this week also complained they were still waiting for relatives to be let out. "We are waiting for the release of our sons. We have been waiting for three days now, since we heard about the pardon of political prisoners," said Mohammed Khaled Khmeira.

"What bothers us most is the lack of information. There is no information from the prison. They told us nothing about how this will be implemented, who will be freed, who will not."

Samir Ben Amor is also concerned that, despite promises from the government, the exact wording of the amnesty law has yet to be released. Although the government has said it will recognise the previously banned Ennahdha Islamist movement, he says many who are still being held are Islamists accused of planning terrorist acts, often with little hard evidence and sometimes with palpably faked witness statements.

Tunisians began three days of mourning today for those who have died during the revolution. Flags were lowered while television stations broadcast recitations of the Qur'an. The government says 78 civilians were killed, many shot by police, in nearly a month of protests over unemployment, corruption and repression that eventually forced Ben Ali to flee.

In a sign of growing normality in Tunisia, which is still seeing daily demonstrations but without the violence that shook the country, the new government said schools and universities would reopen on Monday and sporting events, also on hold since last week, would resume soon.