The department of Ifta issued a statement saying it was the only body in the country authorised to issue fatwas after the Brotherhood's offshoot and the country's main opposition, the Islamic Action Front (IAF), on Sunday banned Muslims from joining non-Muslims in their military presence in Afghanistan. The Jordanian government described the fatwa as "offensive".
"We are the only party to issue edicts on public matters. Nobody asked us to issue a fatwa," the Ifta department said on Thursday.
Jordan, a US ally, has for years maintained silence over its role in Afghanistan. But last year the extent of its involvement was revealed when one of its security agents was killed in a suicide bombing that also killed seven CIA operatives in a military base in Afghanistan.
The Ifta department highlighted the Jordanian army's role in providing help and medical aid in disaster and war-torn areas. It said "no party has the right to question that role".
The government has acknowledged that Jordan operates a field hospital in Afghanistan, but it remains unclear how many Jordanian troops are stationed there.
The fatwa, posted on the IAF's website, said: "Joining the allied forces in Afghanistan and other countries is considered assisting non-Muslims in their aggression against Muslims. This is haram and a [form of] oppression."
The fatwa considered "those who support the Americans and the allied forces in fighting the Muslims, non-Muslims".
The edict seemed to have struck a nerve because it came from IAF religious scholars, said Fouad Hussein, an independent analyst specialising in Islamic movements, and "therefore, it gives it a religious flavour rather than a political one".
It is also came amid growing tensions between the Islamists and the government after the IAF boycotted last month's parliamentary elections to protest against a new electoral law they said was designed to deprive them of votes. They also complained about a gradual loss of democratic gains and civil rights.
"It seems the IAF's fatwa was intended to provoke the government," Mr Hussein said.
Last week, Ayman Safadi, the deputy prime minister and the government's spokesman, defended the army's role in Afghanistan.
"Jordan is proud of the role played by the armed forces and all other security agencies to help our brothers and stand by them, whether in Gaza or Afghanistan or anywhere else in the Arab and Muslim worlds," the state-run Petra News agency quoted him as saying last week.
"Jordan will continue to help and stand by all brothers, including the Afghan people, to surmount challenges, and will do [the] utmost to protect Jordan's security and stability from anyone and anywhere."