The four are accused in connection with the botched NBN-ZTE telecommunications agreement, the Philippine Daily Inquirer reported.
It is the second criminal case filed against Arroyo. The first involves accusations of electoral sabotage.
The court ordered the arrests of former Elections Commission Chairman Benjamin Abalos and former Transportation Secretary Leandro Mendoza along with Arroyo and her husband.
Deputy presidential spokeswoman Abigail Valte said the arrest warrants were a preventive measure to ensure that the accused are in the country while the case is being heard, GMA News reported.
The four are accused of using their positions in government to push through a $329 million national broadband network project with a Chinese firm.
The Arroyo's lawyer Ferdinand Topacio told The Philippine Star the former president and her husband were surprised that a warrant for their arrest was issued.