A young Indonesian leader on Tuesday visited a memorial at MacDonald House, the site of a 1965 bombing, and lay flowers at the monument in Orchard Road.
Dr Dino Patti Djalal, 48, had also laid flowers a day before at the graves of the two marines who carried out the bombing.
He told The Straits Times that his gesture was "to highlight the fact that this issue is sensitive to both nations".
"It's a painful period for both of us. Given the fact that this issue has somewhat recaptured public imagination... I think it's important to do this act of laying the flowers at the graves of Usman (and) Harun (the two marines)," said Dr Djalal, a potential presidential candidate.
Referencing then-Prime Minister Lee Kuan Yew's conciliatory gesture in 1973, when the Singapore leader laid flowers on the graves in Jakarta, Dr Djalal said: "I realise as I look at the issue, one thing that remains to be done is for an Indonesian to pray at the site of the bombing, because these were innocent victims. So this is the purpose of my visit."
His act comes a week after two Indonesian marines posed as the perpetrators of the bombing at an international defence event in Jakarta, prompting Singapore's Ministry of Foreign Affairs to express concern and disappointment.
Indonesia's decision to name a new frigate the KRI Usman Harun, after two marines who were made national heroes in 1968, was publicised last month. It drew protests from Singapore and strained bilateral ties.
Usman and Harun were convicted and executed in Singapore for the bombing that left three civilians dead and injured 33 others.
Dr Djalal stressed that his visit to Singapore was a personal one, and that his laying of flowers was a "people-to-people gesture".
The former Indonesian ambassador to Washington is a participant in the ongoing presidential convention of Indonesia's Democratic Party, and is known to be a close ally of current President Susilo Bambang Yudhoyono, having been a presidential spokesman for foreign affairs.
But he rejected suggestions that his visit had to do with the upcoming legislative elections in Indonesia on April 9, an important precursor to the country's presidential polls in July.
"If this were a political thing I would just play it safe, because this is something that is not going to please everybody," he said.
"But I call this the politics of doing the right thing, and my thesis as an Indonesian young leader has always been that leaders must do not what is popular, but must also shed light on events, and must do the right thing."
He added it was "totally inappropriate" that two Indonesian marines posed as the bombers last week, especially as it was done at an international forum.
During his visit to the Jakarta cemetery on Monday, Dr Djalal had told reporters that describing the duo as heroes was apt, given their total commitment in carrying out their orders.
"Soldiers are never wrong. They carried out their tasks fully," he said.
But the Singaporean victims also have to be honoured because they are civilians who "did no wrong", he added.
He told reporters that the matter was resolved, and Indonesia and Singapore need not reopen an old wound.
"Now Indonesia and Singapore relations have changed totally, they're peaceful. Both Indonesia and Singapore are pillars of Asean," he said then.