Arroyo was served with a warrant in a hospital room, where she will be guarded, the Financial Times reported.
She won't be taken to a detention facility because of a medical condition.
The former leader, under investigation for allegations of corruption and poll cheating, tried to leave the country Tuesday to seek medical treatment abroad for an undisclosed bone ailment. She and her husband were stopped at the Manila airport.
The independent Commission on Elections filed the charges against Arroyo and former top election officers Friday, the Times said. The case centers on allegations that Arroyo rigged the outcome of senatorial elections in 2007.
The Philippine Department of Justice had said it wouldn't object to a hospital arrest for Arroyo, 64, ABS-CBN News reported.
"The condition of where she will be confined does not lie with us or the [Commission on Elections] but with the court," Justice Secretary Leila de Lima said. "Whether it's hospital arrest or house arrest, it is up to the court. We will not object for as long as she does not leave."
Arroyo is charged with ordering large-scale tampering of returns that cheated an opposition candidate out of a victory in the 2007 Senate elections, the BBC reported. Arroyo said she's done nothing wrong.
Arroyo, president from 2001-2010, and her husband were put on a watch list of people who had to ask permission to leave the country, a move she said violated her rights.
The Supreme Court, dominated by Arroyo appointees, twice issued restraining orders in her favor but justice officials said the arrest warrant for Arroyo made the restraining orders moot.