THE Indonesian Foreign Minister, Marty Natalegawa, has directly repudiated comments by the opposition last week that the relationship between his country and Australia was dysfunctional because of the asylum seeker issue.

"I disagree with that," he said after meetings with his Australian counterpart, Bob Carr, in Jakarta yesterday.

Australian Foreign Minister Bob Carr (right) is greeted by his Indonesian counterpart Marty Natalegawa. Credit:Reuters

"The asylum issue is only a third dimension in our bilateral relations, and I'm certainly not going to allow this issue to define the nature of our relations."

The opposition spokesman on immigration, Scott Morrison, said on Friday: "The relationship with Indonesia with this government has become so dysfunctional that we find ourselves in the situation where we bear the full burden [of rescuing asylum seeker boats]".