The anti-graft court dismissed a motion made by Estrada seeking to clear him of plunder charges, arguing that he was illegally ousted from the presidency by a military-backed popular revolt in January 2001.
It also dismissed another motion by Estrada to put his successor, President Arroyo, on the witness stand as part of a strategy to win acquittal on the case.
The Sandiganbayan said the motions were "denied for lack of merit."
Estradas lawyers had asked the court to place Mrs. Arroyo and Chief Justice Hilario Davide on the witness stand to support their contention that Estrada was illegally ousted.
They argued that Davide connived with Mrs. Arroyo to oust Estrada from office even as the presidency had not been officially declared vacant.
Estradas lawyers also requested the Sandiganbayan to summon Defense Secretary Angelo Reyes, Sen. Aquilino Pimentel, and Supreme Court Justices Artemio Panganiban, Antonio Carpio, and Renato Corona. The request was denied.
The Supreme Court had earlier ruled that the presidential succession was legal.
The Sandiganbayan, in its 11-page decision, stressed it did not have the "authority to go behind a final decision of the Supreme Court and question the motives/biases of the justices who rendered such decision."
It said the Sandiganbayan had limited powers over the Supreme Court and any move to "invalidate a final and executory decision of the highest court of the land would be rank absurdity."
The Sandiganbayan pointed out that the Supreme Courts verdicts "are not legally the work of the individual justices" but the product of the Supreme Court "acting as a collegiate body."
"There is only one Supreme Court from whose decisions all other courts take their bearings. Estradas assertions would, indeed, be so abhorrent to the guarantee of stability in the law, in particular and in the state, in particular," the Sandiganbayan stressed.
While the anti-graft court acknowledged that magistrates "are not above the law," and can be "fallible and susceptible to foibles like everyone else," it noted that the law has a procedure for questioning these judicial acts.
"The procedure being followed by (Estrada) in herein case is certainly not" the procedure that needs to be followed for questioning a judicial act, it said.
Estrada lawyer Alan Paguia said it was clear "the ruling did not take into consideration the arguments" presented.
He did not say what their next plan would be.
Estrada, a former movie star, theoretically faces the death penalty if convicted on charges of plunder, illegal use of an alias, and perjury. He is accused of plundering a personal fortune of up to P4 billion during his 30 months in power.
The Sandiganbayan also ruled that the services of the lawyers it appointed to represent Estrada Prospero Crescini, Manuel Pamaran, Noel Malaya, and Irene Jurado will be retained.
It made the ruling after Paguia said he only represented Estrada in the motion to dismiss the charges, and will not present evidence for Estradas defense.
"Under the circumstances, it is prudent, therefore, to retain the services of the counsels de officio if only to assure that (Estradas) right both substantive and procedural are adequately protected," the anti-graft court said.
The Sandiganbayan said the four lawyers "have been zealously and competently assisting (Estrada) in his defense." With AFP report