As groups supporting autonomy and independence began campaigning , a series of pro-integration paramilitary groups of East Timorese began threatening violence — and indeed committing violence — around the country . Alleging pro-independence bias on the part of UNAMET , the groups were seen working with and receiving training from Indonesian soldiers . Before the May agreement was announced , an April paramilitary attack in Liquiça left dozens of East Timorese dead . On 16 May 1999 , a gang accompanied by Indonesian troops attacked suspected independence activists in the village of Atara ; in June another group attacked a UNAMET office in Maliana . Indonesian authorities claimed to be helpless to stop the violence between rival factions among the East Timorese , but Ramos-Horta joined many others in scoffing at such notions . In February 1999 he said : " Before Indonesia withdraws it wants to wreak major havoc and destabilization , as it has always promised . We have consistently heard that over the years from the Indonesian military in Timor . " As militia leaders warned of a " bloodbath " , Indonesian " roving ambassador " Francisco Lopes da Cruz declared : " If people reject autonomy there is the possibility blood will flow in East Timor . " One paramilitary announced that a vote for independence would result in a " sea of fire " , an expression referring to the Bandung Sea of Fire during Indonesia 's own war of independence from the Dutch . As the date of the vote drew near , reports of anti-independence violence continued to accumulate
an April paramilitary attack
Liquiçá Church massacre
Indonesian occupation of East Timor