But the Middle-East based 30 year-old remains equally confident that Ange Postecoglou’s men will improve in time for next month’s visit of Kyrgyzstan to Canberra, after giving up the lead in Group B to Belgian coach Paul Put’s exultant team.
Milligan was perplexed as to how the side, which had taken maximum points from its opening three group games, came so badly unhinged in slumping to a 2-0 loss.
“We won’t change anything and will just continue on the same path," Milligan said.
"No doubt there were areas where we fell short and we will work on them in lead up to the next game.
“We have come a long way in the last 12 months. We didn’t want this result and it feels like a bit of a step back.
“The fortunate thing is there’s another qualification game coming soon and we’ll have the chance to rectify things."
The former Melbourne Victory skipper banished any talk of the Socceroos taking anything for granted against a Jordan side, which had similarly embarrassed them in Amman three years ago.
“It wasn’t about complacency in any way, we were aware of what we were coming to and what we needed to do," he said.
"It's just the case that if you are not switched on and at your very best, these teams can match us.”
Milligan also refuted any suggestions that a boisterous and hyped-up 17,000 crowd at Amman's International Stadium had got under the Socceroos' skins, as a collective lethargy appeared to grip a line-up which lacked the imagination or craft to deal effectively with its bogey team.
“It’s was a wonderful atmosphere and they had a wonderful crowd," Milligan said.
"They are passionate about what they do and we expected that and the crowd had nothing to do with it.
“Obviously it lifts them and the first 10 minutes it gave them an extra leg as such, and an advantage, but we took the sting out of that and got the ball and moved it.
“We were sluggish starting the second-half from the kick-off, not doing what we normally do. We don’t normally go backwards from the kick-off and things went from there.”
Milligan said he couldn't figure out why Australia found Amman such a barren hunting ground.
“I can’t pin-point anything at the moment but the coaching staff will have a look and pin-point where we went wrong," he said.
“First-half we lacked bit of penetration and a killer instinct. We were getting into good areas but not that final area.
"Conceding a goal early in the second-half (to Hassan Abdel Fattah's spot-kick) changed the dynamics of the match.
"We had to push on a bit more and we tried to do that in the way we always play, it’s a strange one but it just wasn’t happening for us.
"A lot of their balls forward were aimless ones, even for the goal that caught us out after the break it was a toe-bash from inside their half, but we should have been aware and dealt with it.”
Though infruriated by late time wasting as Jordan held a one-goal advantage - its second from Hamza Al Daradreh came only six minutes from time – Milligan said it had earned the right to try and hold the lead.
"We’ve been dealing with that type of thing for a long time and I was very aware and the ref was very aware," he said.
"He handed it the way he decided. We tried to keep it moving and they wanted to slow it down and they had every right as they were in front."
