Coach Adnan Hamad was detained at Melbourne Airport by immigration authorities for more than four hours when the team arrived from New Zealand to prepare for their World Cup qualifier with the Socceroos on June 11.
"The Jordanian football association had completed all the entry procedures for the entire members of the delegation in accordance with the diplomatic methods and obtained the formal visas to enter Australia to all members of the delegation," the FA said in a statement on their website (jfa.com.jo).
"The Jordanian football association will ask for official clarifications from the Australian football association and notify the international federation, FIFA, on the matter."
The JFA general secretary Khalil Al Salem said the team needed intervention from the Jordanian embassy to help with the coach's entry into Australia.
Both countries had signed an agreement before World Cup qualifiers to appoint a local representative to meet visiting teams at the airport to help with any such logistical delays, the JFA said.
Jordan and Australia are locked on seven points in Group B of the final round of Asian qualifying for the 2014 World Cup finals in Brazil, with the Socceroos in third spot on goal difference.
Japan (14) have already claimed one of the two automatic qualifying sports for the finals with second-placed Oman on nine points, though they have played one more game than Australia and Jordan.
The team that finishes third in the five-team group can still qualify for Brazil, but must win a two-legged playoff against the equivalent finisher in Group A before another playoff against the fifth-placed team in South America.
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