Police said a large group of people attempted to charge Taur Matan Ruak's campaign headquarters in Dili and when blocked by police, threw stones into the compound.
Taur Matan Ruak's campaign manager called the incident "shameful for democracy" after allegations that Fretilin supporters were involved.
A Fretilin spokesman said there was no proof Fretilin supporters were involved and the incident had been exaggerated as part of a smear campaign against the party.
News that makes sense
Your trusted source for staying up-to-date with the world around you. Get free daily news updates and analysis, straight to your inbox.
The incident comes ahead of the presidential election on Monday, where independent candidate Taur Matan Ruak, known as TMR, is up against Fretilin candidate Francisco Guterres "Lu Olo" for the role of president.
National Police (PNTL) deputy commander Alfonso de Jesus said due to the presence of police the incident was not a serious one.
"We had six police officers there but straight away they are not respecting the police presence there then the group is using the opportunity to take stones and throw them at the office," he said.
Mr de Jesus said the group were out on the road and then tried to charge through into the office, but police blocked them.
No arrests have been made but a police investigation is underway into the incident.
TMR campaign manager Jose Belo said he was in the office when the attack occurred.
"They tried to storm into the compound and there were a lot of stones, they threw stones into the compound, yelling and whatever. It's a shame for our democracy," he said.
Mr Belo said it was lucky there was a police car stopped in front of the main gate and the group was blocked from entering.
Fretilin campaign spokesman Jose Teixeira said the party went to great lengths to cooperate with police for the Fretilin rally yesterday and "any act of violence is abhorrent".
"But considering the history of Timor-Leste this was a very minor incident," he said.
Mr Teixeira said the Fretilin party had been subject to more violence and intimidation than anyone else.
"We reject the allegation our supporters were involved, and we call on the police to thoroughly investigate the incident and prosecute those they feel are responsible."
