Almost two years of relative peace in south Maluku's capital was broken when a hard-line group of Christian separatists, known as RMS, raised their independence flag and marked the anniversary of their movement with a parade through the town on 25 April.
The parade and the failure of police to arrest leaders of the RMS for raising their flag, a highly provocative act in Indonesia, sparked Christian-Muslim clashes. Twenty-four hours later, 20 people lay dead.
But a day after the violence, groups of professional snipers began taking pot shots at police as well as Christians and Muslims, which threatened to turn the contained clashes into full-scale fighting reminiscent of the one that raged for three years.
Between 1999 and 2002, at least 5000 people were killed and half a million others displaced in the sectarian war that pitched Christian militias against Muslim rivals.
However, a government-sponsored peace pact brought a halt to much of the fighting and the militias were disbanded.
But since the RMS celebrated its anniversary, snipers have turned Ambon's streets into death traps.
They are responsible for almost half of the 38 deaths, as well as many more injuries, says Ichsan Malik from an Ambon non-governmental group, the Peace Building Institute.
The United Nation mission office
ablaze in Ambon in April
At least 10 of these snipers are members of the local military command, says Rum Suneth, a former civil servant and researcher at the Peace Building Institute. Suneth says he saw military men he recognises being shot by the security forces during one anti-sniper operation last week.
However, he suspects they were taken to a military hospital for treatment and has not been able to interview them.
Meanwhile, a Western analyst, and expert on the conflict, says police sources have revealed the arrest of at least one police and one military sniper last week.
Nasir Rahawarin, the secretary for the Muslim Clerics Council of Indonesia (MUI) in Ambon, says police informers have told him that a group of former police and military officers carrying out sniper attacks had been arrested.
Unlike previous violence when snipers were aligned with a religious militia, these snipers have been ordered to shoot both Muslims and Christians says Rahawarin, repeating information from a police source.
Such snipers indicate that the violence is the result of long pent up tensions, argue analysts.
"If all the snipers are arrested, then the normal community will not be involved in the conflict any more"
secretary, Muslim Clerics Council of Indonesia (MUI)
"I'm sure it's orchestrated. We just don't know whether it is from Jakarta or Ambon," says the analyst.
The snipers appear to be deployed primarily to prolong and escalate the violence says Rahawarin.
"If all the snipers are arrested, then the normal community will not be involved in the conflict any more."
Police and military spokesmen deny the claims that security forces could be behind the attacks.
Police say they have shot several snipers but those were never arrested because they were rescued by their companions.
Military commander General Endriartono Sutarto said any troops who were found to be participating in the conflict would be tried, adding that the police had no political agenda in Maluku.
And as the Indonesian media reported that the snipers appeared to be using military-issue weapons, military spokesman Sjafrie Samsoedin said the snipers’ guns might have been stolen from a police armoury in 2000.
The police and military commanders have blamed much of this violence on the RMS, arguing it is primarily a conflict between Muslim nationalists and Christian separatists.
The wife and daughter of the separatist leader, Alex Manuputty, who fled to the US, have been arrested and will be charged with treason.
Meanwhile, Ambon's former police chief, Brigadier General Bambang Sutrisno, has been replaced for failing to control the separatists.
Many Indonesians say they would
like a former general as premier
However, some analysts say blaming the continuing violence only on the separatist force, or RMS, is illogical.
"The RMS are only 200 to 300 people. They are not all over Ambon. This is a very extreme group of Christians who are not supported by other Christians," says Pastor Cornelis Bohm, from the Amboina Crisis Centre.
There are several possible reasons as to why the violence may be orchestrated by members of the security forces say analysts.
Rahawarin says they may be have been paid by local thugs running security as well as smuggling and construction rackets during the previous conflict and who are now looking to regain their power.
Alternatively, there are accusations that the conflict may have been ignited or inflamed so that the military can regain control over security in Maluku, which has been under police command since a civil emergency was lifted last September.
Police and military have been fighting for control of Indonesia's provinces, and ever since the police's successful investigation into the Bali bombings, police forces have become far more powerful.
Controlling security in conflict zones such as Ambon, or Aceh, is lucrative for the military, which often receives kickbacks and can control vital industries such as logging or fishing.
Preparations for the July presidential elections may be another reason.
Ex-military figures may be trying to make the civilian government appear incapable of dealing with the country's sectarian and separatist conflicts.
But regardless of the actual motivations, the unrest could impact the campaign of one of the prime candidates in the presidential race - Susilo Bambang Yudhoyono or SBY, and his vice-presidential choice - Yusuf Kalla - who was the architect of Maluku's peace deal point out analysts.
"Who will benefit from this? It’s clear that those in competition with SBY will benefit because Maluku is a big success story for SBY and Kalla," says political analyst Daniel Sparringa from the University of Airlangga in East Java.
Indonesian soldiers undergo
The two main candidates to benefit politically from falling support for Yudhoyono would be either retired general Wiranto or President Megawati Sukarnoputri, says Sparringa.
Wiranto, a former armed forces commander and defence chief, is the presidential candidate for the powerful Golkar party.
Yudhoyono, also a retired general and a recently retired security minister, is quite popular but if he starts to look weak and ineffective, many voters in search of a strong leader with a military background could turn to Wiranto in the July elections, say analysts.
Wiranto's advisors dismiss any accusations against their candidate.
"That's fitnah [slander]," says Tito Sulistio, Wiranto's campaign manager.
A senior editor who refuses to be named, points out that such accusations could be part of a campaign by Wiranto's political opponents to discredit him.
He says non-government groups have been paid to demonstrate about past human rights abuses such as the shooting of student demonstrators by security forces that occurred during Wiranto's rule as armed forces commander.
Recent opinion polls show that many Indonesians prefer an ex-general rather than a civilian as their next president.
This is not be the first time that security forces play a crucial part in Maluku’s violence.
Back in 2000, rogue generals trained and equipped Muslim militia, in particular, the Laskar Jihad, a Java-based organisation.
Analysts then said certain factions of the military backed the militia because they wanted to destabilise Abd al-Rahman Wahid’s government, who was trying to bring the military under civilian control.