Hafedh Ben Salah told AFP in an interview that the defendants included "Al-Qaeda-linked jihadists" who have been battling the Tunisian army near the Algerian border for nearly two years.
Since the uprising that ousted former president Zine El Abidine Ben Ali in January 2011, Tunisia has seen a proliferation of "jihadist militias" suppressed under the former dictator.
These groups have been blamed for a wave of attacks, including the assassination last year of two opposition lawmakers whose murders plunged the country into a protracted political crisis.
Suspected "jihadists" have also launched skirmishes against the army in the remote southern Mount Chaambi area since late 2012, killing dozens of soldiers and police.
In July, militants killed 15 soldiers in the restive border region, the bloodiest day in the army's history.
Other detainees awaiting their trial include suspects who "took part in terrorist acts or were preparing to do so," said Ben Salah.
"Since the revolution, I think there have been no terrorists who stood trial but I think that the first cases will come to court towards the end of the month," he said.
According to the justice minister "there are 1,000-1,020 cases linked to terrorism" in Tunisia and "around 600 suspects jailed for terrorism".
He said police had arrested between 2,000-3,000 people since the revolution but that most suspects were released due to a lack of evidence.
Tunisian security forces played a key role in carrying out the repressive policies of the Ben Ali regime and reform has stalled since the revolution.
The country's stringent anti-terror legislation is also yet to change.Authorities are still following a 2003 law, which has been widely criticised by rights groups as it has been used to repress Islamist opposition to the ousted regime.
But efforts to push an amended anti-terrorism law through parliament have failed even though a draft bill calling for defendants to have certain "guarantees" was submitted to lawmakers for a vote.
The justice minister said the law had so far failed because of a lack of quorum in parliament where it needs the approval of 109 deputies out of the 217-member national assembly.
"The government's position is that this law is a priority," said Ben Salah.Tunisia is to hold legislative elections on October 26 followed by a presidential vote in November.
The minister said he expected the anti-terrorism law to return to parliament two days after the general election.