Speaking over Australias ABC Radio, Downer said he has always been "very understanding" of Mrs. Arroyos decision, but that he was not given a chance to explain himself.
"No, I am understanding, dont get me wrong," he said.
"Were having a longer conversation about it, not just a grab on the TV news. Im perfectly understanding of the dilemma she faced," he said.
Downer said he sympathized with Mrs. Arroyo in having to confront the hostage crisis, and that his previous statement only reflected the stand of the Australian government.
"Weve had many back-channel discussions with both of these countries," he said referring to Spain and the Philippines, which both pulled out their forces from Iraq.
"They know perfectly well what our position is and what Ive said in the last few days is nothing new. Im relaxed about it (reactions from Madrid and Manila). Therell be some controversy for a few days, and then the world will move on, as is always the case," he said.
Downer said Mrs. Arroyos decision can be likened to that of Sophie in the movie, "Sophies Choice," where the lead character was faced with a "diabolical" choice.
"Id be the first to acknowledge the difficult situation she faced," he said. "I have to do what I can to protect the (Australian) people, and she has to do what she believes is right to protect hers."
"We have good and close relations with the Philippines, but our positions just dont coincide. They usually do."
Meanwhile, Presidential Spokesman Ignacio Bunye said the Philippines has asked its allies to move on and stop focusing on the pullout of the Philippine contingent.
"We learn lessons from every international controversy," he said. "It is time to move on."