US defence secretary Ash Carter opposed the decision to commute the prison sentence of Chelsea Manning, who was convicted of espionage for leaking classified information while deployed in Iraq.
He told The Associated Press: "That was not my recommendation.
"I recommended against that, but the president has made his decision."
President Barack Obama has drawn intense criticism from members of Congress and others for the decision he made on Tuesday.
He commuted Manning's 35-year prison sentence to about seven years, including the time she spent locked up before she was convicted. Her sentence is now set to expire on May 17.
At the time Manning committed the crimes she was known as Bradley Manning and was serving as an Army private.
In 2013 a judge convicted Manning of 20 counts, including six Espionage Act violations, theft and computer fraud.
She was sentenced to 35 years out of a possible maximum of 90. She was acquitted of the most serious charge of aiding the enemy, which carries a possible life sentence.
The now 29-year-old native of Crescent, Oklahoma, leaked more than 700,000 classified Iraq and Afghanistan war logs and diplomatic cables in 2010 while working as an intelligence analyst in Baghdad.
Manning also leaked a 2007 video clip of a US helicopter crew killing at least nine men, including a Reuters news photographer and his driver.
The Pentagon later concluded the helicopter crew acted appropriately, having mistaken the camera equipment for weapons.
At a White House news conference in Wednesday, Mr Obama firmly defended his Manning decision, arguing she had served a "tough prison sentence" already.
The president said his decision took into account the fact that Manning had gone to trial, taken responsibility for her crime and received a sentence that he said was harsher than other leakers had received.
He emphasised that he had commuted her sentence, not granted a pardon, which would have symbolically forgiven her for the crime.
"I feel very comfortable that justice has been served," Mr Obama said.
Vice President-elect Mike Pence said Mr Obama's decision was a mistake and called the convicted leaker a "traitor".
Mr Pence said that Manning's actions compromised national security, endangered American personnel and compromised individuals in Afghanistan who were co-operating with US forces.
One name missing from the list of pardons and commutations the White House announced on Tuesday is US Army Sergeant Bowe Bergdahl.
The former prisoner of war is accused of endangering comrades by walking off his post in Afghanistan in 2009, and has asked Mr Obama for a pardon. He was captured by the Taliban and held prisoner for five years.
A pardon would allow Bergdahl to avert a military trial scheduled for April. He faces charges of desertion and misbehaviour before the enemy. The misbehaviour charge carries a maximum penalty of life in prison.
Asked about the Bergdahl case, Mr Carter told the AP: "That one hasn't come to me yet in any way. It's a law enforcement matter, so I really can't comment on it."