Najib Riphat Kesoema was recalled to Jakarta in November when President Susilo Bambang Yudhoyono learned Australia had tapped his phone, and those of his wife and other confidants.
He has been making more frequent trips back to Canberra as negotiations on a new code of conduct have progressed, but the president has now asked him to return for good.
He expects to move back within the coming month.
Asked if the circuit-breaker was this week's phone call from Prime Minister Tony Abbott, who apologised for not attending a planned meeting in Bali, the ambassador said rather the move followed months of work on the code.
"The president and foreign minister have been considering this for a long time," he told AAP.
"It just happens that Mr Abbott recently made a phone call to President SBY."
In Tuesday's phone call, the leaders agreed Mr Abbott should visit Jakarta in June but it's understood no firm date has been set.
It's said the president, whose term in office ends later this year, hopes to depart with his legacy of strong relations with Australia intact.
However the Abbott government's policy of turning asylum seeker boats back to Indonesia remains a controversial issue in Jakarta.
