Speaking from Switzerland, where he is attending the World Economic Forum, Mr Abbott praised the Indonesian President, Susilo Bambang Yudhoyono, but then added that he ''of all people'' understood Australia's motivations.

Mr Abbott, who had promised to rejig foreign policy to be more Jakarta and less Geneva, nonetheless used that European country as the stage to declare Australia would ''continue to do what we are entitled to do to secure our borders''.

"The turnback of asylum seekers who have already crossed the territorial border of any country (including Australia), must be dealt with by that particular country in accordance with the mandate of UN convention, and they must manage the together with UNHCR and IOM [International Organisation for Migration].''

''Stopping the boats is a matter of sovereignty and President Yudhoyono of all people ought to understand ... just how seriously countries take their sovereignty. So we will continue to do what we are entitled to do to secure our borders,’’ Mr Abbott said. That is thought to have been a reference to Indonesian sensitivities over West Papuan independence claims.

Prime Minister Tony Abbott: "Stopping the boats is a matter of sovereignty". Credit:Andrew Meares

Australian National University Indonesia expert Greg Fealy said while the ‘‘logic’’ of Mr Abbott’s comments may have been sound, the tone was likely to be counter-productive, and could see Mr Abbott’s reputation permanently damaged in Indonesia. ‘‘The way in which he said it could easily be seen as Tony Abbott lecturing to President Yudhoyono, and in particular I think he used the term ‘‘ought’’ – that Yudhoyono ‘ought’ to understand, and I think that was unfortunate,’’ he said.

Mr Abbott’s comment about sovereignty strikes at a particularly sensitive part of the Australia-Indonesia relationship, as many in the latter country believe Australia was at fault for the breakaway of East Timor, and that it has a desire to make West Papua independent.

However, Mr Abbott and Dr Yudhoyono have previously discussed the asylum seekers in terms of sovereignty, Mr Abbott last year guaranteeing Indonesian sovereignty as he tackled the boats issue.