He said: "Some people are sheltering the rebels in their homes, we have asked for permission to search them."
"We do not have the intention to kill them. The only way is to co-operate with us."
"We call on the people to contribute to a peaceful solution to the problem. For two years they supported Alfredo [Reinado, slain rebel leader] but what have they got?"
State of emergency
East Timor is in a state of emergency until February 23, following the shooting of Ramos-Horta on Monday.
There has been speculation that Reinado intended to kidnap Ramos-Horta, the president and Nobel Peace Prize winner, who is now stated to be in a serious but stable condition.
The rebels shot and critically wounded him outside his home on Monday. Presidential guards killed Reinado during the attack.
Reinado deserted the army in May 2006 to join about 600 former soldiers who had been sacked earlier that year.
The soldiers complained that they had been discriminated against because they were from the western part of East Timor.
The soldiers' dismissal sparked protests that turned into a wave of violence. At least 37 people died and about 150,000 people fled from their homes.