In recent weeks four youth from Oecusse selling food in Rai Kosu were attacked.
The Fretilin leader called for a thorough police investigation into the violent and discriminating behavior.
Alkatiri said all people of Timor-Leste had a right to move freely around the country and earn a livelihood.
"Oecusse people must have freedom of movement,” Alkatiri told reporters on Saturday. “No one must forbid the freedom of people."