INDONESIA has warned Australia it may take concerns about potential spying from the embassy in Jakarta to the United Nations.

The warning, from Indonesian Foreign Minister Marty Natalegawa, has come after media reports Australians agencies may be using embassy offices in Jakarta to spy on Indonesian officials.

Mr Natalegawa, in a televised address, called for a strong commitment from both Australia and the United States that they would not engage in activities "inconsistent" with friendly relations.

The warning has aired doubts about the strength of Australia-Indonesia relations, after Prime Minister Tony Abbott's declarations he wanted a "Jakarta, not Geneva" approach to foreign affairs.

Mr Natalegawa also questioned whether Australia has circumvented existing co-operative agreements to conduct the alleged spying.

It is understood Foreign Minister Julie Bishop sought to satisfy Indonesian grievances about the media reports in meetings earlier this week.