Evalyn Ursua, the lawyer who represented the Filipina raped by Lance-Corporal Daniel Smith, filed a complaint of contempt against the interior and justice ministers, alleging that they violated a court order to keep Smith in a jail in Manila when they handed him over to US custody.
Smith is appealing against his conviction and 40-year prison sentence.
Arroyo said on Tuesday: "I wish to appeal for understanding from the people that this action will not affect the substantive issues at bar, nor impede justice and the rule of law."
But Filipinos are outraged over the government's inability to assert its sovereignty and protect its judicial independence from US pressure.
Renato Reyes, the secretary-general of Bayan (New Patriotic Alliance), a grassroots group, said the manner in which the transfer happened "is provoking another constitutional crisis".
"This is totally unprecedented in the history of the Philippines to put a person convicted of rape under the custody of a foreign authority.
"This raises the question of judicial independence coming under executive pressure," he said.
"The US has virtually slapped us in the face. If it is proven that Mrs Arroyo had directed the transfer, some lawyers have said that that would provide grounds for impeachment."
Ronaldo Puno, the interior secretary, said the government had no choice but to hand him over because it had to respect a bilateral military pact.
"We are telling the world that we are complying with our treaty obligations," he said.
The US embassy announced on Tuesday that Washington has decided to proceed with the annual Balikatan war games with the Philippine armed forces. The US had cancelled the large-scale military exercise last month.
Smith's lawyers, the Philippine government and the American embassy petitioned for his transfer to US custody based on the 1998 Visiting Forces Agreement (VFA) signed by Washington and Manila.
The VFA governs the conduct of US troops in the Philippines.
But Ursua said on Monday: "We all have differing interpretations of the VFA, but in our legal system, in our rule of law, our courts have the final say and under our law, each prisoner is under the jurisdiction of the court.
"Nobody can jail a person and nobody can release a person from detention if there is no court order. That is a very basic rule in our law."