The opposition leader's comments come after the High Court ruled on Friday that an asylum seeker deemed a security risk can still be granted a refugee visa.
In the decision, a majority of High Court judges overturned a regulation that specifies that an asylum seeker deemed a security risk by the Australian Security Intelligence Organisation (ASIO) can't be granted a protection visa.
The decision has important implications for some 50 mostly Sri Lankans given adverse ASIO security assessments who are in indefinite detention in Australia.
Mr Abbott said stopping the boats was the best way to avoid the problem the High Court pointed to.
"It's yet another complication for a government that has comprehensively mishandled border protection policy," he told reporters in Sydney on Saturday morning.
He reaffirmed his calls for the government to reinstate the coalition's full suite of border protection measures including temporary protection visas.
