Ibrahim Halawa has been detained in an Egyptian prison for more than three years.
His trial was adjourned for a 17th time on Tuesday.
Charlie Flanagan said the government's focus was on supporting an application for Mr Halawa to be deported.
The Irish government has also requested that he be considered for release under a new Egyptian government amnesty scheme for young prisoners.
Mr Halawa, who turned 21 on Tuesday, is the son of Ireland's most senior Muslim cleric and was arrested during anti-government protests in Cairo in August 2013.
He has been charged along with 463 others with inciting violence, rioting and sabotage relating to the protests in Cairo.
Mr Halawa appeared in court on Tuesday and told judges that he was innocent and asked to be allowed to return home.
His family has denied claims that Mr Halawa is a member of the Muslim Brotherhood, Egypt's oldest and largest Islamist organisation.
The Egyptian government has declared it a terrorist group, a claim the organisation rejects.
More than 1,000 people have been killed and 40,000 are believed to have been jailed since President Abdul Fattah al-Sisi led the military's overthrow of Mohammed Morsi, Egypt's first democratically elected head of state, in 2013.

On Friday, a 34-year-old woman became the second person in three weeks to die at the busy Bow Roundabout junction.
The victim, who is yet to be named, was pronounced dead at 16:45 GMT.
The 29-year-old driver of a lorry involved in the crash was arrested on suspicion of causing death by dangerous driving.
He was released on bail to return to an east London police station on 7 December pending further inquiries.
The London Cycling Campaign (LCC) group demanded an immediate redesign of the roundabout.
It said the roundabout was dangerous because the cycle superhighway stopped in the middle of the Bow roundabout.
LCC's chief executive Ashok Sinha said: "We're appalled at this latest preventable death and are fearful of what may happen when large numbers of cyclists are expected to tackle this junction on their way to and from the Olympics next year.
"We can't understand how this junction can form part of what is one of the Mayor's flagship cycling projects: it must be redesigned now."
TfL surface transport manager Leon Daniels said: "We are extremely sorry to learn of the tragic death of a female cyclist, following a collision with an HGV on the Bow Road roundabout on Friday evening.
"Our thoughts are with her family and friends. I have visited the scene and both TfL and the police have launched inquiries which will report as quickly as possibleâ€¬."  Â 
Last month a 58-year-old man was killed in a collision with a tipper truck.
Four priority lanes for cyclists, branded cycle superhighways, have been painted blue around London, and another eight are due to open within the next four years.
On Saturday, more than 300 cyclists rode through the capital in a "Tour du Danger" protest calling for the capital's roads to be made safer.
Cycling blogger Danny Williams said: "I think the superhighways should be made proper superhighways.
"I think it's a good idea, incredibly badly implemented and not very well thought through, and the Mayor needs to take responsibility for that.
A TfL spokesman said: "There has been an 18% fall in the number of cyclists killed or seriously injured on London's roads in the last decade, compared to the TfL's baseline figures from the mid to late 1990s."
No-one from the office of Mayor Boris Johnson was available for comment.

The bodies of Ronald Kidd, 40, and Holly Alexander, 37, were discovered at a tenement in Rosefield Street, in the city's west end, at about 21:00 on Sunday.
The property was sealed off by police while detectives and scenes of crimes officers investigated.
The man is expected to appear at Dundee Sheriff Court on Wednesday.
Detectives said a review of CCTV in the are was being carried out, while house-to-house inquiries are continuing.
Police have also appealed for anyone with information to come forward.
Det Insp Brian Geddes, who is leading the investigation, said: "I would be keen to hear from anyone who heard or saw anything suspicious in the Rosefield Street area, in the days between Thursday 8 December 2016 and Sunday 11 December 2016."
The Irish foreign minister has said the government will apply maximum pressure on the Egyptian authorities to secure the return of a prisoner to Ireland.
[NEXT_CONCEPT]
Transport for London (TfL) has said it is "sorry" about the death of a female cyclist who was killed on a cycle "superhighway" in east London.
[NEXT_CONCEPT]
A 37-year-old man has been charged in connection with the deaths of a man and woman at a Dundee flat.