Arroyo's lawyers questioned the charges during oral arguments, and the court said it would take a second look.
The former president, who is suffering from a neck ailment, was detained for about eight months in a government hospital in a separate election sabotage case before she posted bail in July. She has also posted bail in another case against her that stems from a botched overpriced deal with a Chinese telecommunications company.
She has accused her successor, Benigno Aquino III, of pursuing a political vendetta.
Aquino has accused Arroyo of graft and promised to rid the Philippines of corruption. His ratings remain high, and the cases against Arroyo and her inner circle are meant to highlight the Aquino administration's determination to restore public and investor confidence in government.
Officials have denied Arroyo's request to seek medical treatment abroad, saying she may not return to face the charges.
Arroyo's lawyer Anacleto Diaz said today that the witnesses against her had no personal knowledge of the transactions of the Philippine Charity Sweepstakes Office. The charges allege that money from the agency's intelligence funds was diverted for personal gain from 2008 until Arroyo stepped down in 2010.
Both of the other cases are ongoing, with witness testimony under way.
Diaz told reporters that the court suspended the arrest warrant against Arroyo and nine others, but Clerk of Court Ella Teresita Rosete denied that.
Special Prosecutor Diosdado Calonge said the warrant would be implemented unless it is recalled by the anti-graft court or stopped by the Supreme Court.
Court Sheriff Albert dela Cruz said he released the arrest orders to police and other law enforcers today.
The nine other people are mostly former senior officials of the lottery agency. The charges against them and Arroyo are punishable by life imprisonment, with no bail allowed.
Prosecutors alleged in court documents that Arroyo conspired with lottery officials and government auditors "to surreptitiously divert public funds sourced from PCSO's operating budget for personal gain."
Manila: The Philippine anti-graft court on Thursday ordered the arrest of former President Gloria Macapagal Arroyo in the third corruption investigation against her, this one accusing her of misusing USD 8.8 million in state lottery funds during her last years in office.
First Published: Thursday, October 04, 2012, 14:56