Minister of State for Media Affairs Mohammad Momani said the government stands with the family of the Jordanian pilot captured by the self-proclaimed IS.
"When we entered the US-led coalition against the IS, we knew there will be losses such as some taken hostages or even martyrs. We will continue our war on terror and to defend the homeland," Momani said in an interview at the state-run Jordan TV.
The captured pilot is the first troop in the US-led coalition to be captured in the four-month war against IS.
A senior Jordanian military official confirmed the pilot was seized, saying his plane went down in Syria's Raqa region, a militant stronghold, early on Wednesday.
"The pilot was taken hostage by the IS terrorist organisation," official news agency Petra quoted the official as saying.
Jordan did not say why the plane went down, but both the jihadists and a monitoring group said it was shot with an anti-aircraft missile.
If confirmed, it would be the first coalition warplane shot down since air strikes on IS began in Syria in September.
Doubt over how Jordanian warplane crashed in Syria
The United States dismissed a claim by the Islamic State militant group that it had shot down a Jordanian F-16 fighter flying with US-led coalition forces, which crashed in eastern Syria.
"Evidence clearly indicates that ISIL did not down the aircraft as the terrorist organization is claiming," said US Central Command, the body overseeing the coalition air war over Iraq and Syria.
The statement did not give a cause for the "crash," and confirmed the lost jet's Jordanian pilot had been taken captive by IS guerrillas.
"We strongly condemn the actions of ISIL, which has taken captive the downed pilot," said CentCom commander General Lloyd Austin.
"We will support efforts to ensure his safe recovery, and will not tolerate ISIL's attempts to misrepresent or exploit this unfortunate aircraft crash for their own purposes."
"The Jordanians are highly respected and valued partners and their pilots and crews have performed exceptionally well over the course of this campaign," he added.
Family of pilot informed of his capture
Earlier, the Syrian Observatory for Human Rights, a Britain-based monitoring group, said its sources in Syria confirmed IS had captured the pilot "after shooting his plane down with an anti-aircraft missile near Raqa city."
Coalition warplanes have carried out regular strikes around Raqa, which IS has used as the headquarters for its self-declared "caliphate" after seizing control of large parts of Syria and Iraq.
The IS branch in Raqa published photographs on jihadist websites purporting to show its fighters holding the captured pilot.
One showed the pilot, wearing only a white shirt, being carried from a body of water by four men. Another showed him on land, surrounded by about a dozen armed men.
A photograph was also released of the pilot's military identification card, showing his name as Maaz al-Kassasbeh, his birth date as May 29, 1988, and his rank of first lieutenant.
The jihadists claimed to have shot down the warplane with a heat-seeking missile.
The pilot's father Youssef was quoted by Jordanian news website Saraya as saying the family had been informed by the air force of his capture.
He said the military promised it was "working to save his life" and that Jordan's ruler, King Abdullah II, was following events.
The Sunni extremist IS has committed widespread atrocities in areas under its control, including mass executions of captured soldiers and public beheadings of hostages including Western journalists and aid workers.
Jordan's military says one of its warplanes has crashed while on a mission over Syria and the pilot has been captured by the Islamic State group.
