Transport was not arranged for Rev Hassan Abduraheem and Rev Kuwa Shamal (above), as well as a third co accused Abdulmonem Abdumawla.
Their hearing went ahead without them where a judge confirmed the charges against them and set a date for the next hearing on 21 August.
Accusations range from waging war against the state to entry and photography of military areas and equipment.
In total they face seven charges, two of which can be punishable by death.
Rev Abduraheem has been detained since December 2015, while Rev Shamal has been held since May 2016.
Lawyers for the men have already raised concerns about their treatment after they were moved prisons to a building much further from their families.
Christian Solidarity Worldwide's Chief Executive Mervyn Thomas said: "We are seriously concerned that the trial of Reverend Abduraheem, Mr Abdumawla and Reverend Shamal began in their absence.
"The serious charges levelled against Reverend Abduraheem and Mr Abdumawla...have no foundation or merit.
"We call on the Sudanese Government to ensure that this trial is conducted with respect to Fair Trial Principles, which includes at the minimum ensuring that the men are present at every hearing, and have regular access to legal representatives and family members.
"We also urge the government to end the harassment and targeting of religious and ethnic minorities by NISS, and to uphold the civil rights of every Sudanese citizen."
