Indonesia's Armed Forces commander says the decision to name its new frigate after the two marines behind a 1965 bombing in Singapore was agreed upon over a year ago.
"We agreed on the name on 12 December 2012, after long discussions. There is no correlation with recent developments," General Moeldoko told reporters in Parliament on Monday.
"The naming is not intended to stir emotions. We did not think of that," he added.
Gen Moeldoko's comments came amid speculation that Indonesia's decision to name the ship KRI Usman Harun - after marines Osman Mohamed Ali and Harun Said - was deliberate, or timed near upcoming elections.
The name was only publicised more widely this year and picked up in a Kompas report on Feb 4, sparking concerns from Singapore which views the two marines as terrorists for bombing MacDonald House in Orchard Road in 1965. Three civilians were killed and 33 persons injured in the bombing.
The two marines were convicted and hanged in Singapore in 1968. Indonesia later gave them a full military funeral.
Gen Moeldoko said Indonesia viewed these men differently.
"Osman and Harun are Indonesian marines who have been named national heroes," he said.
"I cannot accept them as terrorists. They are state actors," he added.
He also said others had a right to take issue with the ship's name, but stressed that Indonesia would not change its decision.
The bombing of MacDonald House was the worst of 42 explosions in Singapore by Indonesian saboteurs during Konfrontasi, the Indonesia-Malaysia Confrontation that lasted from 1963 to 1966.
Then-President Sukarno had opposed the formation of Malaysia, which had included Singapore.
Meanwhile, both Gen Moeldoko and Defence Minister Purnomo Yusgiantoro sought to downplay Singapore's cancellation of invitations for 100 Indonesian officers to the Singapore Air Show, as well as a meeting this week between Indonesia's Deputy Defence Minister Sjafrie Sjamsoeddin and Singapore's Second Minister for Defence Chan Chun Sing.
Gen Moeldoko and Mr Purnomo told reporters separately they did not think the ongoing row would affect bilateral relations.
"Neighbours will be there forever," Mr Purnomo said.
"They cancelled the invitation, we did not go. It's as simple as that," he said, when asked if Indonesia was offended.
"Let's not make it complicated."
