The turn-back of two groups of asylum seekers on Monday has put further strain on the Australia-Indonesia relationship after Indonesian Foreign Minister Marty Natalegawa launched another stinging criticism of the Abbott government's boats policy. .

Indonesian officials confirmed that two boats of asylum seekers were intercepted by Australian naval or Customs vessels in recent days and their 20 passengers put together onto one wooden vessel and pushed back towards Indonesian waters.

Indonesian Foreign Minister Marty Natalegawa, pictured with his Australian counterpart Julie Bishop, says "issues" remain between the two countries. Credit:Tatan Syuflana

Dr Natalegawa said there were a few “issues” between the two countries, but that the boat policy remained a problem.

“[The existence] of a problem has been confirmed by the return [this week],” Dr Natalegawa said.