Foreign Secretary Jalil Abbas Jilani said Pakistan had told the US that Afridi was involved in "criminal activities" that violated the laws of the land.
Addressing a news briefing in Washington on Prime Minister Nawaz Sharif's ongoing visit to the US, Jilani said the doctor was "not a hero and was facing cases in courts".
Pakistan also told the US that the Lashkar-e-Taiba had been banned and action could be taken against its founder, Hafiz Mohammad Saeed, if substantial evidence is made available, he said.
Responding to questions after the US House Committee on Foreign Affairs demanded the release of Afridi, Jilani said that the Pakistani courts would decide his fate.
The demand for Afridi's release was raised during a meeting between the US House Committee and a Pakistani delegation that included Finance Minister Ishaq Dar, Jilani and Sartaj Aziz, the premier's Adviser on Foreign Affairs and National Security.
Afridi was arrested shortly after the May 2, 2011 raid by US commandos that killed bin Laden. He was subsequently convicted by a court in the tribal belt on a charge of treason for alleged ties to the Lashkar-e-Islam militant group.
On August 29, a judicial official overturned the 33-year jail term given to Afridi and ruled that the judge in the tribal areas had exceeded his authority when he handed down the sentence last year. The official also ordered a fresh trial.
The US has been pressing Pakistan to release Afridi, who ran a fake vaccination campaign in Abbottabad to gain access to bin Laden's compound.