His supporters say the charges are politically motivated and an attempt to prevent him from standing in next month's parliamentary polls.
They have called for nationwide protests demanding his release.
Reporters will not be allowed access to the courts martial proceedings, being held in the headquarters of the Sri Lankan navy, where Fonseka is curently being detained.
On Monday, Sri Lanka's former chief justice accused the government of acting unconstitutionally by prosecuting Fonseka behind closed doors using military law, rather than using the normal legal system which allows open hearings.
"The arrest detention of General Sarath Fonseka is contrary to articles 13-1 and 13-2 of the constitution, the code of Criminal Procedure, the International Covenant on Civil and Political Rights and Universal Declaration of Human Rights," Sarath Silva told reporters in Colombo.
"It is also contrary to the Army Act and the Chief of Defence Staff Act."
Officials in Rajapaksa's government have accused Fonseka of plotting a coup and the assassination the president, although those accusations will not form part of the court martial.
Former close allies, Rajapaksa once referred to Fonseka as a "national hero" for his role in leading the Sri Lankan military in its final victory over Tamil Tiger rebels.
The defeat of the Tigers in May last year brought an end to more than two decades of bloody civil war.
But the two men fell out shortly after over who should take credit for the victory.
Fonseka has refused to attend the preliminary hearings for the courts martial and reports say he will also stay away once the case begins on Tuesday.
However officials at his Democratic National Alliance party said that he would be represented by a team of lawyers.