Christian groups tried to block the admiral's car as he arrived in Ambon for a series of meetings with military officials in the city.
The protesters, who were calling for an end to sectarian violence on the islands, also tried to stop him leaving.
Addressing several hundred troops at the battalion headquarters, Admiral Widodo said the conflict between the Christian and Muslim communities was far from over.
But he said, it had to be resolved, with the security forces showing absolute impartiality.
The admiral was met by the military chief of the Moluccas, General Max Tamaela, on his arrival.
General Tamaela was threatened with the sack on Sunday, along with the governor of the islands, Saleh Latuconsina.
The Indonesian President, Adburrahman Wahid, said he would soon replace the two men for failing to contain the violence in the Moluccas.
Alleged military involvement
The islands have been wracked by violence between Christians and Muslims since January 1999.
Both communities have accused the army and the police of taking sides.
In particular, soldiers have been accused of helping the Muslims, whilst the police are alleged to have sided with the Christians.
The Indonesian security forces continue to step up attempts to reduce the violence in the Moluccas.
The navy on Friday announced it had deployed warships and spotter planes to blockade the Moluccan Islands to try to stop weapons being imported into the area.
The army has also poured in nine new battalions of troops and launched house to house searches for weapons since taking over security from the police last week.
Tens of thousands of refugees have fled the sectarian violence, seeking refuge in army camps or elsewhere in Indonesia.
More dead discovered
Admiral Widodo left Ambon for the northern island of Halmahera, where it is believed some of the worst violence of recent weeks has taken place, with reports that hundreds of people have been killed.
Muslim aid workers on the island said they had now found many more bodies inside mosques which have been burned down.
The aid workers said they had been told by the military to bury the bodies, which had been there for about 10 days.
"It is very difficult to count the bodies ... [they] were torched and burned by unidentified people," said Mursal Amal Tomagola of the Medical Emergency aid group.
The BBC's correspondent in Ambon, Richard Galpin, says independent sources also report serious fighting on the nearby island of Seram with up to 200 people killed.
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