The officer, Army Lt. Col. Paul Almanza, called a recess 30 minutes into Friday's proceeding at Fort Meade to consider the request.
The hearing is to determine whether Manning will face a court-martial.
Almanza's civilian occupation as a Justice Department prosecutor was the chief reason defense lawyer David Coombs gave in asking him to recuse himself. The Justice Department is conducting a criminal investigation targeting WikiLeaks founder Julian Assange.
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?"
Manning, 23, is charged with aiding the enemy by leaking hundreds of thousands of secret documents that ended up on the anti-secrecy website.
Almanza, who is an Army reservist, said he hasn't formed an opinion about Manning's guilt or innocence.
The hearing is to determine whether Manning should be court-martialed. If his case goes to trial and he is convicted, he could face life in prison. The government has said it would not seek the death penalty.
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."
Dressed in his camouflage Army fatigues and wearing dark-rimmed eyeglasses, Manning sat at the defense table showing little expression. He occasionally twirled a pen between his thumb and finger.
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 members of the news media were allowed to enter.
A U.S. military legal expert told reporters shortly before the proceedings began Friday that the presiding officer is likely to make his recommendation on whether to court-martial Manning within eight days after the hearing ends. The hearing is expected to last over the weekend and possibly well into next week.
The legal expert, who could not be identified under Army ground rules, said Manning is to be present for all proceedings, including sessions closed to the public for consideration of classified material.
Fort Meade, located between Washington and Baltimore, is, ironically, home to U.S. Cyber Command, the organization whose mission includes protecting computer networks like the one Manning allegedly breached by illegally downloading huge numbers of classified documents in Iraq.
He is suspected of giving the documents to WikiLeaks, the anti-secrecy website that last year began publishing the materials.
Manning's lawyer asserts that the documents' release did little actual harm.
The case has spawned an international movement in support of Manning, who is seen by anti-war activists as a hero who helped expose American mistakes in Iraq and Afghanistan. To others he is a villain, even a traitor, who betrayed his oath of loyalty by deliberately spilling his government's secrets.
Manning's supporters planned to maintain a vigil during the hearing and were organizing a rally for Saturday.
The hearing at Fort Meade is intended to yield a recommendation to Army Maj. Gen. Michael S. Linnington, commander of the Military District of Washington, on whether Manning should be court-martialed. Linnington could choose other courses, including applying an administrative punishment or dismissing some or all of the 22 counts against Manning.
The Manning case has led to a debate over the broader issue of whether the government's system for classifying and shielding information has grown so unwieldy that it is increasingly vulnerable to intrusions.
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, who turns 24 on Saturday, 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.
Last month, 54 members of the European Parliament signed a letter to the U.S. government raising concerns about Manning's 18-month pretrial confinement.
It took months for the Army to reach the conclusion that Manning was competent to stand trial. In the meantime Manning's civilian lawyer, Coombs, has sought to build a case that appears to rest in part on an assertion that the government's own reviews of the leaks concluded that little damage was done.
Associated Press writer Matthew Lee contributed to this report.