He was speaking on a one-day visit during which he met Muslim and Christian leaders from the islands, wracked by three years of violence which has left thousands dead and or displaced.
Islamic militants marked the visit by Mr Haz, who heads Indonesia's largest Islamic political party, by publicly surrendering arms to government officials in the capital, Ambon.
Critics say Mr Haz is trying to shore up support among hard-line Muslim groups ahead of the 2004 election.
In a visit to the village of Soya, where masked attackers killed 12 Christians in April, Mr Haz said the killings must not be repeated.
"That deadly incident is not what we all want, it's a bitter experience and shouldn't happen again," he said.
"To any groups who want to ruin the Moluccas' security situation and condition either from inside or outside the Moluccas, we will take stern measures against them," the vice president said in Ambon.
Reconciliation hopes
The vice president donated 100m rupiah ($11,400) to Soya for the reconstruction of its church, which was torched during the attack in April.
The governor of the Moluccas, Saleh Latuconsina, said Mr Haz's visit was a boost for public morale, showing that Jakarta was concerned about ending the religious conflict in the islands.
"Both communities have started to communicate and mingle with each other, the barriers have melted and people are resilient to issues and provocative things," he added.
Christians and Muslims in the Moluccas used to live peacefully.
But in January 1999 violence erupted between the two communities, sparked by a minor traffic accident in the main city of Ambon.
The violence intensified in mid-2000, with the arrival of the Islamic militia Laskar Jihad.
Radical contacts
Mr Haz leads the Islamic-based United Development Party and has courted controversy by recently meeting leading Islamic radicals.
On Tuesday, he toured a school and medical clinic in Soya run by Laskar Jihad.
The group is accused of fuelling religious strife in Maluku and central Sulawesi, and some analysts link it to Osama Bin Laden's al-Qaeda militant network.
Laskar Jihad also handed over hundreds of weapons including daggers, machetes, guns and homemade bombs - a gesture aimed at meeting long-ignored conditions of a peace deal signed in February.
Mr Haz defended the head of another Muslim militia group, Habib Rizieq Shihab of the Front for the Defenders of Islam (FPI), whom he had met on a previous visit.
The group is accused of making violent raids on nightspots and gambling parlours in the Ambon.
"Habib Rizieq is not a hardliner as many accuse him to be," said Mr Haz, who has had talks with the FPI leader. said.
In May, Mr Haz met Muslim cleric Abubakar Ba'asyir, who has been linked by Singapore and Malaysia to regional terrorism, and he has visited Laskar Jihad's leader, Jafar Umar Thalib, in prison.