"We know that they know of our operations," he told SBS.
"One of the main listening stations that monitors Indonesian communications for years now, every Christmas, gets a message from their Indonesian counterparts wishing them best wishes for Christmas."
Professor Ball said it was highly likely Australia had been monitoring the calls of the Indonesian President Susilo Bambang Yudhoyono, in the same way the US had been monitoring German Chancellor Angela Merkel’s phone.
"Without question from time to time that monitoring activity includes the conversations of the highest levels of the political leadership in Jakarta. There can be no question about that," he said.
Indonesia's Foreign Minister has described alleged spying in Australia's embassy in Jakarta as "outside the norm" amid warnings the claims of espionage could damage relations.
Marty Natalegawa on Friday sought an explanation from Australian Foreign Minister Julie Bishop following claims the embassy had been involved in electronic surveillance in Indonesia, including targeting "political, diplomatic and economic interests".
Dr Natalegawa said that while it was accepted that countries had the capacity to conduct surveillance operations, the Australian spying described in media reports earlier this week was considered to be "outside the norm".
"I'm not sure what's the right term in Australian terminology, I guess it's not cricket to do these kinds of things," Dr Natalegawa said after his "frank and candid" meeting with Ms Bishop in Perth.
"Countries may have capacities, technical capacities to intercept and carry out activities that have been reported and information may have been gathered.
"But whether you would want to put that into effect and therefore potentially damage the kind of trust and confidence that has been nurtured and developed over many decades and years, is something that we may want to ponder."
LISTEN: Monash University Indonesia expert Greg Barton speaking to World News Australia’s Kristina Kukolja
Asked about any similar Indonesian espionage activity, Dr Natalegawa said his country had "ways and means of gaining information".
"We do things in a manner that is proper and in accordance with diplomatic practice," he said.
The meeting, on the sidelines of the Indian Ocean Rim summit in Perth, came as Australia's Ambassador to Indonesia Greg Moriarty met officials in Jakarta after being summoned to answer questions over the spying claims.
Mr Moriarty, who met with Indonesian Foreign Ministry Secretary-General Budi Bowoleksono for about 20 minutes, described the talks as positive but refused to provide any details.
"It was a good meeting and now I have to go and report to my government," Mr Moriarty said as he emerged from the Foreign Ministry.
But the head of the Indonesian parliament's foreign affairs commission, Mahfudz Siddiq, warned that the revelations of spying had the potential to damage relations between Jakarta and Canberra.
"Indonesia must give strong signal, a warning that any country should not do anything that would harm the relationship between two countries," he told AAP on Friday.
The Indonesian Foreign Ministry had earlier issued a statement saying surveillance like that described in media reports would be "considered a serious breach of security which cannot be accepted".
"The conduct as reported was not at all reflecting the spirit of friendly relations," the statement issued on Thursday evening said.
It's been claimed that Australian surveillance collection facilities are in place at embassies in Jakarta, Bangkok, Hanoi, Beijing and Dili, and high commissions in Kuala Lumpur and Port Moresby.
The top secret Defence Signals Directorate operates the listening posts at embassies without the knowledge of most Australian diplomats, according to documents released by US whistleblower Edward Snowden and statements from a former Australian intelligence officer.
The documents revealed the existence of a signals intelligence collection program - codenamed STATEROOM - conducted from sites at US embassies and consulates and from the diplomatic missions of other intelligence partners including Australia, Britain and Canada.
Earlier this week, Dr Natalegawa called in the US embassy's charge d'affaires to protest over reports that the Americans had conducted electronic surveillance and phone-tapping from their Jakarta embassy.
