The criticism, which follows another rebuke of the turn-back plan from Foreign Minster Marty Natalegawa this week, comes just days before Abbott meets President Susilo Bambang Yudhoyono in Jakarta.
Andy said Indonesia had co-operated with Australia in attempting to disrupt people-smuggling operations, but it now faced an unfair share of the burden in dealing with the flow of asylum-seeker boats.
"Even though we have done our best to prevent them, it's impossible for us to stop all of the boats from entering Australia," he said. "This is additional burden for Indonesia. We could've just let them sail to Australia, but no, we respect Australia's wishes.
"This is a dilemma. If we don't save them, then everyone will be blaming us for not respecting human rights ... But if we let them [sail to Australia] then Australia would be yelling at us why we let them go."
The Coalition has repeatedly said its new suite of border protection measures, including the turn-back plan and paying Indonesian villagers for information on people-smuggling operations, were non-negotiable.
Foreign Minister Julie Bishop has said many times the Coalition would not be "seeking permission" to implement its asylum-seeker policies despite Jakarta labelling some of them an attack on Indonesian sovereignty.
- AAP