The United States has said it is "disappointed" by Theresa May's decision to block the extradition of Gary McKinnon and has insisted the extradition treaty between Britain and the US is "fair and balanced".
McKinnon was accused by US prosecutors of "the biggest military computer hack of all time" but he claims he was simply looking for evidence of UFOs.
On Tuesday the home secretary intervened to stop extradition of the the 46-year-old, who has Asperger's, humanitarian grounds.
A spokeswoman for the US Department of Justice told The Huffington Post UK that the Obama administration disagreed with the decision but viewed it as an "exceptional" case.
"The United States is disappointed by the UK Home Secretary’s decision not to extradite Gary McKinnon, particularly given the past decisions of the UK courts and prior Home Secretaries that he should face trial in the United States," she said.
"We note that the Home Secretary has described this case as exceptional and, thus, this decision does not set a precedent for future cases.
"The Home Secretary has acknowledged that Mr. McKinnon is accused of serious crimes and that the United Kingdom’s Director of Public Prosecutions will now consider whether Mr. McKinnon has a case to answer in a UK court."
McKinnon's case has led many in Britain to question the fairness of the extradition treaty with the United States. Critics argue it is easier for the American government to extradite British citizens than it is for the UK to extradite American citizens.
A review conducted by Sir Scott Baker for the Home Office decided the Extradition Act was not biased against British citizens.
However a separate review conducted for Nick Clegg by former Lib Dem leader Sir Ming Campbell concluded it was unfair.
"The proper course should be to raise the British standard to the American one, so that UK citizens do not suffer a disadvantage compared to their US equivalents," Sir Ming said.
On Tuesday May announced that she would introduce a "forum bar", as called for by Sir Ming, in extradition cases which would mean a court hearing has to be held to decide whether a person should stand trial in the UK or abroad.
However she told MPs that Sir Scott's overall view that the treaty was fair was "broadly sound", a statement welcomed by the United States.
"Our extradition relationship with the United Kingdom remains strong, as is demonstrated by the extradition of five alleged terrorists from the United Kingdom just last week," the administration spokeswoman told HuffPost UK.
"At the same time, we are pleased that the home secretary has accepted the finding of Sir Scott Baker’s independent panel that the U.S.-UK extradition treaty brings benefit to both countries.
"The United States fully agrees with the report’s conclusion that the treaty is fair and balanced.
She added: "The law enforcement relationship between the United States and the United Kingdom has always been predicated on trust, respect, and the common goals of protecting our nations and eliminating safe havens for criminals.
"Our extradition treaty serves the interests of both our nations, and the United States values our continuing collaboration with British law enforcement authorities on a myriad of shared concerns."
May has been widely praised for blocking McKinnon's extradition, which many saw as a case of the British David standing up to the American Goliath.
However former Labour home secretary Alan Johnson questioned whether the move would damage UK-US relations, suggesting it was merely done to increase the popularity of the government.
Johnson told MPs he thought May had made the decision "in her party's best interest; it is not in the best interests of the country".