Several police officials were lightly wounded in the pre-dawn raid on a house in the northern Jordanian city of Irbid, the Petra news agency reported.
A unit comprised of elite police and intelligence forces stormed the cell's hideout because of "information on plans by Al Qaeda targeting the Jordanian arena," Petra said, quoting an unidentified security official. It did not elaborate.
Security officials told The Associated Press that the two men opened fire at the special security forces that came to arrest them.
Police shot one man dead, said the officials, who spoke on condition of anonymity because the operation was under way. The other man is in police custody, they said.
Petra said suspect Suleiman Ghayad al-Anjadi was holding a temporary Jordanian passport when he was killed on the spot. It did not say what was his nationality of origin, but temporary passports are usually granted to Palestinians.
The detained suspect is a Jordanian man named Ramadan Mustafa al-Mansi, Petra said.
The operation, which began at 5 a.m. local time, ended seven hours later, officials said. It was not immediately clear if other people were arrested.
The security officials said al-Anjadi, the suspect who was killed, was on the police most wanted list of Al Qaeda terrorists.
Last April, military prosecutors charged al-Anjadi with helping Al Qaeda ring leader Azmi al-Jayousi escape from jail, according to military court documents. Police had thwarted the escape plot and put al-Anjadi on trial in absentia in the military State Security Court for his role in the bungled attempt.
The military court sentenced al-Jayousi to death last year for a 2004 plot to attack sites in Jordan by setting off a cloud of toxic chemicals that would have killed thousands of people. Authorities said the plot also targeted the U.S. Embassy, the prime minister's office, and various intelligence and military court officials.
Jordan, a close U.S. ally, has arrested scores of Islamic militants for plotting militant attacks.