The director of Becora prison, Joao Domingos, said the inmates escaped from the facility in the capital, Dili, after Mass on Sunday.
Prime Minister Xanana Gusmao inspected the prison afterward and ordered security forces to capture the inmates as soon as possible. Hours later, 13 of them were recaptured in a hilly region on Dili's outskirts, Domingos said.
He said one of two guards who were attacked was hospitalized in critical condition.
Domingos said Juga Gama, a famous 24-year-old singer who was sentenced to 20 years last month in a drug case, was believed to be the mastermind of the escape. Gama escaped and is still missing.
It was the second escape from the prison since the August 2007 escape of rebel soldier Alfredo Reinado, who was imprisoned for deserting the army. Reinado was later fatally shot by presidential guards during a February 2008 attack on the compound of then-President Jose Ramos-Horta.