The hearing is to determine whether Manning will face a court-martial on charges that he aided the enemy by leaking hundreds of thousands of classified military and diplomatic documents.
Almanza is a Justice Department prosecutor in civilian life, and Manning's lawyer said that was reason enough to step aside. The Justice Department is conducting a criminal investigation targeting WikiLeaks founder Julian Assange.
After Almanza denied the request that he step aside, Manning's lawyers said they would seek to appeal that decision to the Army Court of Criminal Appeals. It was unclear when the court would decide whether to hear the appeal.
Before that dispute, Manning, who turns 24 on Saturday, took notes during at his hearing at this Army base between Washington and Baltimore. Dressed in Army camouflage fatigues and wearing dark-rimmed glasses, Manning sometimes twirled a pen in his fingers as the hearing got off to a slow start.
A U.S. military legal expert told reporters shortly before the proceedings began that Almanza was likely to make his recommendation on whether to court-martial Manning within eight days after the hearing ends. The hearing is expected to last through the weekend and possibly well into next week.
The decision on whether to go to court-martial will be made by Army Maj. Gen. Michael S. Linnington, commander of the Military District of Washington. Linnington could choose other courses, including applying an administrative punishment or dismissing some or all of the charges.
While David Coombs, Manning's civilian attorney, pushed for Almanza, to step aside, Capt. Ashden Fein, a member of the prosecution team, told the presiding officer, "The United States does not believe you've exhibited any bias in any form and that you can render a fair and impartial decision."
The Manning case has spawned an international support network of people who believe the U.S. government has gone too far in seeking to punish the Pfc.
Manning's supporters planned to maintain a vigil during the hearing and were organizing a rally for Saturday. By midday Friday, about 50 protesters had assembled outside the military base's main entrance, and a few dozen marched down an adjoining road carrying orange signs that read, "The Bradley Manning Support Network."
About 30 people were able to go to a base movie theater, where they could watch closed circuit video of the courtroom proceedings, according to Jeff Patterson of the Manning support group. Retired Army Col. Ann Wright, an adviser to the group, was able to sit in the courtroom, but Patterson said he did not know whether Manning's family or other supporters were able to attend the hearing in person.
In addition to the question of bias, Coombs also argued that Almanza had wrongly denied a defense request to call as witnesses the "original classification authorities" who first decided to classify as secret the material WikiLeaks published. Instead, Almanza has chosen to accept unsworn statements from those people, Coombs said.
Coombs said the decision eliminated the defense's ability to question why the leaked material was classified.
"Let's put witnesses on the stand," he said. "Why is this stuff classified? Why is it going to cause harm?"
During the hearing's opening moments, Manning responded to a series of questions from Almanza. After summarizing the charges against Manning, Almanza asked if he understood them. "Yes, sir," Manning replied.
Asked whether he had any questions about the charges, Manning replied, "No, sir."
The hearing is open to the public but with limited seating in the courtroom. A small number of reporters were present but not allowed to record or photograph the proceedings. Manning was not seen arriving in the courtroom because he was brought in before journalists were allowed to enter.
Absent from the Meade proceedings will be Assange, who runs WikiLeaks from England. He is fighting in British courts to block a Swedish request that he be extradited to face trial over rape allegations.
A U.S. grand jury is weighing whether to indict Assange on espionage charges, and WikiLeaks is straining under an American financial embargo.
The materials Manning is accused of leaking include hundreds of thousands of sensitive items: Iraq and Afghanistan war logs, State Department cables and a classified military video of a 2007 American helicopter attack in Iraq that killed 11 men, including a Reuters news photographer and his driver.
At the time, Manning, a native of Crescent, Okla., was a low-level intelligence analyst in Baghdad.
Manning was detained in Iraq in May 2010 and moved to a Marine Corps brig at Quantico, Va., in July. Nine months later, the Army sent him to the military prison at Fort Leavenworth, Kan., after a series of claims by Manning of unlawful pretrial punishment.
When it filed formal charges against Manning in March 2011, the Army accused him of using unauthorized software on government computers to extract classified information, illegally download it and transmit the data for public release by what the Army termed "the enemy."
The first large publication of the documents by WikiLeaks in July 2010, some 77,000 military records on the war in Afghanistan, made global headlines. But the material provided only limited revelations, including unreported incidents of Afghan civilian killings as well as covert operations against Taliban figures.
In October 2010, WikiLeaks published a batch of nearly 400,000 documents that dated from early 2004 to Jan. 1, 2010. They were written mostly by low-ranking officers in the field cataloging thousands of battles with insurgents and roadside bomb attacks, plus equipment failures and shootings by civilian contractors.
A month later, WikiLeaks released hundreds of thousands of State Department documents, including candid comments from world leaders.