Aquino, 39, is charged with conspiracy and acting as an unregistered foreign agent. If convicted, he faces up to 10 years in prison.
He remains detained and could face new charges in the months to come, said Michael Drewniak, spokesman for Newark prosecutor Christopher Christie.
Assistant US Attorney Karl Buch told US District Judge William Walls he expected to file additional charges against Aquino.
"The indictment that stands today is not the indictment that the government will go to trial on," Buch said during the arraignment. He did not specify what the additional changes might be.
Buch asked the judge for a nine-month adjournment because of the complexity of the case, the continuing investigation, and the sensitivity of the classified evidence.
Buch argued it would take months for Aquino’s lawyers to get security clearances to view much of the evidence, which includes classified documents, and for federal agencies to clear the documents for review.
To date, more than 150 documents are considered classified and that number will "significantly rise" as the government’s investigation continues, Buch said.
Walls disagreed and ordered both sides to return to court Jan. 17 for a status conference. No trial date was set.
"We are pleased the judge did not rubber-stamp that request," Aquino’s lawyer, Mark Berman, said.
Lawyers for both sides agree Aquino, now a nursing student in New York, received documents from Leandro Aragoncillo, 46, an analyst of the Federal Bureau of Investigation (FBI).
"He definitely had documents, had information from Aragoncillo," Berman said, but reiterated his claim that nothing was marked as classified, and Aquino had no reason to believe they were.
"Mr. Aquino is innocent," he said.
Clad in a green jail uniform and shackled at the wrists and ankles, the former deputy director of the Philippine National Police did not speak during the hearing.
Aquino was also a senior superintendent of the now-disbanded Presidential Anti-Organized Crime Task Force.
The espionage case has caused a political scandal in the Philippines. According to the FBI complaint, the documents were reportedly used by opponents of President Arroyo to try to unseat her.
Aquino supported opposition Sen. Panfilo Lacson, who lost last year’s presidential election to Arroyo. Lacson, a former national police chief, has acknowledged receiving information from Aquino, who served under him.
Excerpts of the FBI documents have been published in the Philippine press, including one that said, "Arroyo has always exhibited paranoia and the need to control every aspect of the Philippine economy and politics."
Mrs. Arroyo has accused her political foes of trying to oust her from office and damaging relations with the United States.
Aragoncillo, a former Marine who used to work in the White House, has been in plea negotiations. That leaves the possibility that Aquino could face the charges alone. He has not been indicted and has yet to make his court appearance.
Aquino, who rejected a plea deal, had known Aragoncillo for about a year, Berman said.
Aquino, who had been living in New York, was arrested in September and indicted on Oct. 6. Acting as an unregistered foreign agent carries a sentence of up to 10 years and a $250,000 fine.
An FBI complaint accused Aragoncillo of the same offenses as Aquino, along with unauthorized use of a government computer, which carries a sentence of up to 10 years and a $250,000 fine.
Aragoncillo is a naturalized US citizen who was born in the Philippines.
The 21-year Marine veteran worked from 1999 to 2001 at the White House as a military security official and was assigned to the vice president’s office under both Al Gore and Dick Cheney.
Aragoncillo became a civilian employee of the FBI in July 2004 in New Jersey. He began sending classified information and documents in January, including some to Aquino, according to the FBI complaint. He was suspended by the FBI after his arrest in September.
US government officials said the FBI is investigating whether Aragoncillo took classified information from the White House.
Officials from the FBI and the Central Intelligence Agency believe Aragoncillo’s case is the first espionage case involving the White House in modern history.
The Philippine Department of Justice had earlier ordered an investigation into possible links between opposition leaders and Aragoncillo.
The order from Justice Secretary Raul Gonzalez to the National Bureau of Investigation directed the bureau to look into any links, especially the "money trail coming from the Philippines to Mr. Aragoncillo and Aquino, which will eventually establish the conspiracy between the duo and the supposed ranking Filipino officials."
Malacañang vowed to unmask the identities of Filipino opposition politicians involved in the espionage case.
Mrs. Arroyo heaped scorn on the opposition, branding them as "robbers" and "coup plotters."
Several opposition leaders including deposed President Joseph Estrada earlier said they received information from Aquino but have insisted it was not confidential and the information was "shallow."
Lacson, Senate Minority Leader Aquilino Pimentel, Sen. Jinggoy Estrada and Parañaque Rep. Roilo Golez have admitted communicating with Aquino. — AP, AFP