Melbourne – East Timor would work with former military chief General Wiranto if he is elected Indonesian president despite his alleged war crimes, the fledgling state's first lady said Monday.

Wiranto was last week selected as the presidential candidate for the Golkar Party, which ruled Indonesia for 35 years under former President Suharto.

Wiranto has been indicted by United Nations-backed prosecutors in East Timor for backing militias who terrorised East Timor following the 1999 independence referendum in 1999 when he was Indonesia's top military officer.

Kirsty Sword-Gusmao, the Australian wife of East Timor President Xanana Gusmao, said the relationship between the two countries would not be harmed if Wiranto won the presidency in July.

"I don't think it would be significantly more challenging than with Megawati at the helm," Sword-Gusmao said, referring to current Indonesian President Megawati Sukarnoputri. "And I don't think that there's any reason to believe that Wiranto is any more hostile to East Timor's sovereignty than any other leader."

But she conceded Wiranto's election would be difficult for some East Timorese given the violence which dominated the vote for independence five years ago.

In the months surrounding the vote, pro-Jakarta militias killed an estimated 1,400 people, burned towns to the ground, destroyed 80 percent of the former Portuguese territory's infrastructure and forced or led more than a quarter of a million villagers into Indonesian-ruled West Timor.

"Clearly, he is linked emotionally to the violence [of] 1999, but I don't see that as being a huge impediment to building a constructive relationship between the two countries," Sword-Gusmao said. Indonesia is due to go to the polls elect its president on July 5.

Sword-Gusmao is winding up a two-week tour here to promote the ALOLA Foundation, an organisation she started which cares for women and children in East Timor.