Authorities are preparing to appoint a new police commander amid a new push to rid the force of corrupt and undisciplined officers.
But evidence of a flare-up in regional tensions, between those from the country's east and west, have authorities concerned.
An inflammatory leaflet has been circulating in the capital, Dili, warning: "If a person from the east is appointed as commander, we will petition and organise people from districts to go against the government".
East Timor was torn apart in 2006 when east-west tensions sparked deep divisions in the armed forces and ultimately triggered violence that left at least 37 people dead and around 150,000 displaced.
The unrest prompted countries including Australia to send in troops to restore order.
Government sources and one UN official believe the leaflet was written by a group of officers within the police force. It includes threats of violence and calls for early elections if anyone from the east is appointed police commander.
The International Crisis Group (ICG) said the development was "deeply concerning".
"As we have seen before, if this sense of discrimination and resentment is left to fester it can cause serious problems down the track," ICG analyst in East Timor Anna Powles said.
Former prime minister Mari Alkatiri, who now leads the opposition Fretilin party, said the threats mirrored the kind of tensions that led to the 2006 violence.
"In 2006 they started with this kind of thing - the pamphlets and letters dividing the people," he said.
But unlike in 2006, there are 1,500 UN police and almost 1,000 Australian and New Zealand troops deployed in East Timor.
UN police are taking the emergence of the leaflet seriously and trying to confirm its source.
"We pay attention to any information regardless of classification," Acting UN police commander Juan Carlos Arevalo said.
State Secretary for Security Francisco Gutteres believes the leaflet was written by officers who will be hurt by a new promotions system aimed at wiping out corruption and nepotism.
"I am quite sure that more than 80 per cent of the police are quite supportive of the new changes," he said.
But there are other signs of problems within the police force.
Members of the Task Force Unit recently threatened to strike over a pay dispute, leading to a heated confrontation at police headquarters.
And the Prosecutor-General Longuinhos Monteiro last week revealed that the interim head of the police, Alfonso de Jesus, was being questioned in relation to disciplinary issues.