Indonesia's Armed Forces Commander, General Moeldoko, said it was incorrectly reported that he had made an apology over the naming of a navy frigate after two Indonesian marines behind a 1965 bombing in Singapore.
Dr Moeldoko told reporters on Thursday that his comments, in an interview with Singapore broadcaster Channel NewsAsia aired on Tuesday, were misunderstood.
"Saying sorry that the naming of the Usman Harun is our final decision, does not mean saying sorry. If things are twisted, that's normal for reporters," he said.
"There was no apology. What I meant was: 'sorry, the naming of the Usman Harun is our final decision'."
Dr Moeldoko's latest remarks came as several Indonesian Members of Parliament and observers criticised him for saying sorry, adding that this harmed Indonesia's dignity and insulted the memory of national heroes.
Marines Usman Haji Mohamed Ali and Harun Said were convicted for the bombing at MacDonald House in Singapore's Orchard road 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.
But Indonesia's decision to name the frigate after the marines drew protests from Singapore, and Singapore ministers told their Indonesian counterparts the move would reopen old wounds.
Indonesian ministers, however, maintained that the naming of the vessel was in line with the navy tradition of naming ships after the country's heroes, and that no ill will was intended.
In the TV interview, Dr Moeldoko said: "We have no ill intent whatsoever to stir emotions. Not at all." He added that "there are sensitivities that we did not foresee and it escalated". He also said "relations between the two countries are on the mend".