At a pre-trial hearing Sunday, Judge Adam Arif reportedly granted a conditional release based on their treatment during detention and the state’s failure to respond.
The hearing was scheduled to hear a motion from defence lawyers seeking their release from custody.
Ishag Ali was charged with attempting to carry out a terrorist attack and Hussain Afeef was charged with planning to carry out a terrorist attack.
At Sunday’s hearing, the state submitted two more audio analysis reports as evidence to prove they were working in collaboration with the terrorist group Islamic State.
They face a jail sentence of up to 20 years if found guilty.
Last month, two suspects charged with terrorism in connection with a separate bomb plot were freed on medical grounds.
The two men were among four arrested in April last year for allegedly planning bomb attacks in five areas of the capital city. They were also accused of working with the IS group.
Closed hearings have been taking place since charges were pressed in July.
A US-based security and risk management consultancy estimates around 200 to 250 Maldivians are known to be fighting in Syria and Iraq, making the island nation the highest per capita foreign fighter contributor.
Earlier this year Defence Minister Adam Shareef said the number of Maldivians travelling to Syria to fight with jihadist groups was rising.
He put the figure at 61, up from the previous number of 49.
The Global Terrorism Index 2017 from the Institute for Economics and Peace observed the Maldives was “grappling” with the challenge of returning foreign fighters who may radicalise others or attempt attacks.
“The country has little experience with counterterrorism and has hundreds of soft targets such as hotels perched on atolls in the Indian Ocean,” it said.
An anti-terror law was passed in 2015 after the outgoing administration was accused of ignoring the threat posed by jihadi recruitment since the first reports of Maldivians joining terror groups emerged in 2013.
At least six Maldivians fighting with the al-Qaeda-affiliated Al-Nusra Front in Syria are believed to have been killed in battle.
In July this year, a Maldivian man fighting with the IS in Syria was beheaded by Maldivian fighters in the rival terrorist group Tahrir al Sham.