JAKARTA (Reuters) - Three people, including two police officers, were killed in Indonesia’s easternmost province of Papua after alleged separatists opened fire on boats carrying voters and officials who had just cast ballots in local elections, police said.

Indonesia had been on high alert for violence with elections for 171 city mayors, regents, and provincial governors held across the world’s biggest Muslim-majority country on Wednesday.

Indonesia took control of Papua following a widely criticized U.N.-backed referendum in 1969, six years after the end of Dutch colonial rule.

Alleged separatists on Wednesday shot at two boats carrying voters and officials on a river in Torere district in Papua, killing three people, police said on Thursday. Three more police officers were missing.

The incident comes just days after a suspected separatist shooting at a tiny airport in Nduga district in Papua where three people were killed and a child injured. The election for that district’s chief had to be postponed due to the violence.

Unofficial counts in Indonesia’s regional elections put candidates favoring President Joko Widodo ahead in three provinces on Java island, home to more than half of the population of the world’s third-largest democracy.

But candidates backed by the opposition fared better than expected in the elections, which is an important pointer for national parliamentary and presidential races in 2019.

Some hardline Islamic leaders have publicly called for the ousting of Widodo, who has pledged to protect Indonesia’s tradition of pluralism and moderate Islam in the officially secular country.

Widodo is expected to run again for the presidency in 2019, against retired general Prabowo Subianto, who was narrowly defeated in the last presidential vote in 2014.