Press secretary Karine Jean-Pierre told reporters on Monday that Biden had “wrestled” over the decision during the family’s Thanksgiving break on the island of Nantucket, Massachusetts, at the weekend.
The Democratic president issued the pardon on Sunday evening before heading off on an official trip to Africa.
Ms Jean-Pierre told reporters on Air Force One en route to Angola: “He believes in the justice system, but he also believes that the raw politics infected the process and led to a miscarriage of justice.”
Ms Jean-Pierre said Biden believed Hunter was “singled out” because of who he is and that “they [the president’s opponents] would continue to go after his son”.
“This is why the president took this action,” she added. As recently as last month, Ms Jean-Pierre was still telling reporters that Biden would not pardon his son.
In June, Hunter Biden became the first child of a sitting US president to be criminally convicted after a jury in Delaware found him guilty of three charges for lying about his drug use on a form when buying a handgun.
In September, he also pleaded guilty to federal tax charges that included failure to file and pay his taxes, tax evasion and filing a false return.
The pardon – which covers any potential federal crimes that he may have committed between January 2014 and December 2024 – spans a period beyond the tax and gun offences.
It dates back to the year in which he became a board member at Ukrainian energy company Burisma – a period when his father, then US vice-president, had a key role in American policy towards Kyiv.
This period was the focal point for a congressional inquiry in which Republican lawmakers accused Biden of lying when he denied involvement in his son’s business dealings, though their impeachment effort fizzled. Biden has denied wrongdoing.
US First Lady Jill Biden said on Monday from the White House: “Of course I support the pardon of my son.”
The president’s decision sparked furious reaction from Donald Trump and other senior Republicans, who have long accused the Biden administration of “weaponising” the justice department against their enemies.
On his Truth Social social media platform, Trump said that the executive clemency was an “abuse and miscarriage of justice”.
House of Representatives Speaker Mike Johnson said that “trust in our justice system has almost been irreparably damaged by the Bidens and abuse of it”.
Criticism from Democrats – who have regularly accused Trump of disregarding the rule of law – was more muted.
“President Biden’s decision put personal interest ahead of duty and further erodes Americans’ faith that the justice system is fair and equal for all,” Colorado Senator Michael Bennet posted on X, formerly Twitter.
Congressman Greg Stanton, an Arizona Democrat, rejected Biden’s claim that the case was unfair.
“This wasn’t a politically motivated prosecution,” he said. “Hunter committed felonies and was convicted by a jury of his peers.”
Neama Rahmani, a former federal prosecutor, told the BBC that he believed Biden had misled the American people.
“President Biden was disingenuous this entire time when he said that he would not pardon his son,” Mr Rahmani said.
“A pardon was the plan from the beginning, but President Biden misled the American people because he, then Kamala Harris, were in the middle of an election.”
When he takes office in January, Trump will not be able to rescind his predecessor’s pardon, said Mr Rahmani.
The president’s power to pardon people is “absolute”, he said.
“There is nothing Donald Trump or the Republicans can do to stop it,” Mr Rahmani added.