Singapore will accept Indonesia's apology over the naming of a new warship at "face value", stressing that both countries have to find ways to move beyond it, Defence Minister Ng Eng Hen said on Sunday.

He was responding to clarifications by Indonesia's Armed Forces Commander, General Moeldoko, who said on Thursday that he did not apologise over the naming of a new navy frigate Usman Harun, after two Indonesian marines behind a 1965 bombing in Singapore.

The general had said in a television interview with Channel News Asia this week: "We have no intent whatsoever to stir emotions. Not at all... I apologise." But on Thursday, he claimed that the media had "twisted" what he said and he had merely said sorry for Indonesia's "final decision" to name the warship.

Dr Ng told reporters at the sidelines of a community event on Sunday that Singapore should not be drawn into the latest development. "It is not productive to get involved in their domestic politics," said Dr Ng.

He acknowledged that Singaporeans may feel perplexed or even upset over the twists and turns, but emphasised that it is important to focus on what the country believes and stands for. "We sometimes may not fully understand the ways of others," he noted.

Moving forward, the minister said that it is vital for both countries to move beyond the incident and rebuild ties based on mutual respect of each other as equal, sovereign nations. "I am confident we can rebuild trust and confidence that has been built up over many, many decades," Dr Ng said.