Defence Minister Ng Eng Hen said he welcomed Indonesian armed forces commander's apology over the naming of a new frigate after two marines responsible for the MacDonald House bombing in 1965.

The Singapore Armed Forces (SAF) will resume bilateral cooperation with the Indonesian Armed Forces (TNI), he said in a statement on Wednesday.

"I welcome General Moeldoko's apology as a constructive gesture to improve bilateral defence ties between our two countries. The SAF will reciprocate General Moeldoko's positive intentions by resuming bilateral cooperation and activities with the TNI so as to strengthen the mutual understanding and friendship that has been built up over many decades," he said.

Gen Moeldoko's apology is the first by an Indonesian military official. "We have no ill intent whatsoever to stir emotions. Not at all," he told Channel NewsAsia in an interview. "I apologise." But he said that the name of the ship would remain the KRI Usman Harun.

The two marines, Osman Mohamed Ali and Harun Said, were convicted for the MacDonald House bombing that killed three civilians and injured 33. They were executed in Singapore in 1968, prompting tensions with Indonesia, which called them heroes and buried them with full military honours. Both sides closed this chapter in 1973 when then Prime Minister Lee Kuan Yew sprinkled flowers on their graves during a visit to Jakarta.

The move to name the new frigate after the two marines drew protests from Singapore, and Singapore ministers told their counterparts the move would reopen old wounds. Defence Minister Ng Eng Hen told Parliament in February the ship would not be allowed to stop at Singapore ports or naval bases, and it would not be possible for the SAF to sail alongside or train with the KRI Usman Harun.

Indonesian ministers had maintained that the naming was in line with the navy tradition of naming ships after the country's heroes, and that no ill will was intended.