On one of the motions, the anti-graft court rejected a request from defense lawyer Manuel Pamaran for the prosecution to make a more detailed presentation of its evidence.
"The court has punctiliously gone over the prosecutions formal offer of exhibits and finds that the purposes stated therein are specific enough for Estrada et al to be guided accordingly in making their objections and clear enough for the court in its determination of the admissibility of the documents as offered," the anti-graft court ruled.
On the other motion, the Sandiganbayan likewise rejected a move to have one of the prosecutors, Alex Padilla, cited for contempt.
Defense lawyers accused Padilla of "misrepresentation" for presenting a witness in a hearing when he was already an undersecretary of the Department of Health and no longer a prosecutor.
Although the court denied their motion, it warned Padilla not to commit the same mistake again.
"He must count himself (fortunate) that no serious injury has befallen the court. We bewail Padillas lack of candor, prudence and foresight. The least Padilla could have done is to follow up his status before conducting the direct examination," the court warned.
"Suffice it to say that Padilla and the entire prosecution panel have been less than honest in their dealings with the court," it said.
The prosecution rested its case in May and the defense was scheduled to start presenting witnesses and evidence June 2.
However, the trial was delayed six times mainly because of a defense motion filed by Estrada through his personal lawyer Alan Paguia, which sought a dismissal of the plunder charges against Estrada.
The Sandiganbayan had rejected the motion.
Estrada said he would not present evidence, maintaining he was illegally ousted from the presidency in 2001 and has parliamentary immunity.
He is on trial for allegedly running an illegal gambling racket, embezzling state funds and profiting from insider trading.
Prosecutors accuse Estrada of amassing more than P4 billion during his 31-month rule and stashing the proceeds in a secret local bank account. Estrada denies the charges.
Theoretically, Estrada could get the death penalty if convicted.
Paguia said the Supreme Court erred when it swore in President Arroyo after declaring the presidency vacant during the January 2001 uprising that toppled Estrada.
Estrada had asked Congress last month to impeach eight Supreme Court justices, including Chief Justice Hilario Davide Jr., for allegedly playing partisan politics to legalize his ouster.
In rejecting Paguias motion, the Sandiganbayan said a lower court cannot directly or indirectly overturn a ruling made by the Supreme Court, the countrys highest tribunal.
One of Estradas court-appointed lawyers, Prospero Crescini, has asked the Sandiganbayan to allow him to quit the case following "irreconcilable" differences with Paguia.
Crescini disagrees with Paguias tack for the defense not to present evidence and rebut the plunder charges against Estrada.
He said the defense has evidence to win an acquittal. Crescini described Paguias strategy as "prejudicial and dangerous," likening it to a "lawyer who is escorting his client to the death chamber."
Although the Sandiganbayan has yet to decide on Crescinis motion, it would have no bearing on the trial because Estrada has other lawyers.