The Timorese government completed the expulsions of the last few dozen Muslims on Wednesday - all of whom considered themselves East Timorese.
The deportees had lived in East Timor before it split from Indonesia during a bloody independence ballot five years ago.
The issue has struck a sensitive cord in Indonesia, the world's most populous Muslim nation, where some local media have described the deportations as a move by predominantly Catholic East Timor against Islam.
Jakarta does not consider the deportees Indonesian nationals.
East Timor, which has a Muslim prime minister and has sought to build good ties with Indonesia, says the issue has nothing to do with religion.
Immigration officer Carlos Geronimo said the evicted Muslims built houses and schools adjacent to the al-Nur mosque, but none had proper East Timorese permits.
"Today, we sent home 184 people. Apart from the ones who were sick, we have sent them all home," said Geronimo, referring to the group who were evicted from shelters around the mosque in capital Dili.
East Timor became formally independent in May 2002 after centuries of Portuguese colonial rule, 24 years of Indonesian annexation and more than two years of UN transitional administration.
An overwhelming vote by Timorese in August 1999 to break free from Jakarta triggered a rampage by gangs supported by elements in the Indonesian army.
The UN estimates about 1000 people were killed in violence surrounding the vote.