The decision by Egypt's Court of Cassation to overturn a life sentence against deposed President Mohamed Morsi was a move to show that the judicial system would not "fully kowtow to the government line", according to Dr Anthony Billingsley, international relations lecturer at the University of NSW.
The court ordered a retrial in the case that revolves around accusations of espionage with Palestinian group Hamas.
The court last week overturned a death sentence against Morsi in a separate case, meaning he no longer faces execution.
Democratically elected after the 2011 uprising, Morsi was overthrown in mid-2013 by Abdel Fattah al-Sisi following mass protests against his rule, and was immediately arrested.
He remains in jail on separate convictions.
"It’s very interesting, the courts have shown themselves to be, on one hand very willing to do whatever they think the president would like," Dr Billingsley told SBS.
"So we’ve seen some extraordinary actions (that are) highly political such as the Peter Greste case, the treatment of the Muslim Brotherhood and the arrest of large numbers of people."
"On the other hand, the court has also shown over many years, including the Mubarak era that it’s got a certain degree of independence and that it refuses to fully kowtow to the government line, even when the court is stacked with a number of government appointees.
"So we are seeing this very erratic behaviour. The decision that Morsi was found guilty of – condemned to death for a prison break – is clearly nonsense."
Morsi was one of 22 high-ranking Muslim Brotherhood officials and supporters convicted last year of spying for fellow-Islamist group Hamas.
The Court of Cassation's ruling on Tuesday overturns all convictions in the case, including life sentences against Mohamed Badie, the General Guide of the Muslim Brotherhood and 15 others.
Senior Brotherhood officials Kheirat al-Shater and Mohamed al-Beltagi as well as Morsi aide Ahmed Abdelatti, who had originally been sentenced to death in the case, also saw their convictions dropped on Tuesday.
"The court will have in the back of its mind, public hostility to what the government has been doing," Dr Billingsley said.
"It (court) will also be conscious of significant divisions within the leadership structure. The president is not exercising power as ruthlessly and as effectively as a lot of people thought he would when he took over.
"He doesn’t have full control of the system as we thought. I think the courts are the leading edge of this wavering of elite unity."
Since toppling Morsi and winning a presidential election the following year, Sisi, a former general, has crushed dissent.
Security forces killed hundreds of Morsi supporters in a single day in 2013, in one of the bloodiest incidents in the country's modern history.
Thousands of Muslim Brotherhood supporters have since been detained and hundreds have received death sentences or lengthy prison terms in mass trials condemned by human rights groups as legally flawed and politically motivated.
The Egyptian government says it does not interfere in the work of the judiciary. Egypt's judiciary says it is independent.
The government deems the Brotherhood, Egypt's oldest Islamist movement, a terrorist group. The Brotherhood says it is committed to peaceful activism.
-With Reuters
