JAKARTA, April 20 (Reuters) - East Timor President Jose Ramos-Horta denied on Sunday that he had linked Indonesia's army to an attack on him after Jakarta said such a suggestion could hurt ties between the countries.

The 58-year-old Nobel laureate nearly lost his life when he was shot twice after gunmen loyal to rebel leader Alfredo Reinado launched early-morning attacks on the president and Prime Minister Xanana Gusmao in Dili in February.

Ramos-Horta said his remarks on Thursday, upon his return home from Australia, that investigations indicated the involvement of elements within Indonesia in Reinado's action had been misinterpreted. He said he had not blamed the Indonesian government or military.

"I always said individuals in Indonesia, and individuals can be of East Timorese origin although they might already be Indonesian citizens," Ramos-Horta said after mass in a Dili church.

"I never said the Indonesian public or TNI." TNI refers to the Indonesian armed forces.

His remarks came after Indonesian President Susilo Bambang Yudhoyono said that East Timor should stop hinting that Indonesia was involved in the attacks as this could hurt relations between the two countries.

Yudhoyono made the comment on Friday while announcing the arrest of three East Timorese soldiers in Indonesia in relation to the attacks on Ramos-Horta and Gusmao. The three had entered Indonesia illegally, he said.

Indonesia invaded East Timor in 1975 and annexed East Timor later that year, maintaining a huge and sometimes harsh military presence and fighting rebels for more than two decades.

East Timorese voted overwhelmingly to split from Indonesian rule but some pro-Jakarta voters say the referendum was rigged by the U.N., despite the presence of numerous independent observers who concluded the ballot was largely fair.

Indonesia's military was accused of backing pro-Jakarta militia groups that went on a rampage in East Timor before and after the independence vote. About 1,000 East Timorese died during the post-vote mayhem, the UN estimates.

East Timor became fully independent in May 2002 after a U.N. transitional administration.

As Asia's youngest nation, East Timor has been unable to achieve stability since its hard-won independence from Indonesia, despite its oil and gas resources.

The East Timor army tore apart along regional lines in 2006, when about 600 soldiers were sacked, triggering factional violence that killed 37 people. (Reporting by Tito Belo, editing by Sugita Katyal and Sanjeev Miglani)

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