"The accusations against her are serious and complex, so this is going to take a lot of time," Foreign Minister Alfredo Moreno told CNN Chile from Thailand on Wednesday.
Chilean press reports said the woman, identified as Gisella Carcamo, and her Tunisian husband Radwan Hamidi assaulted a Syrian military checkpoint.
Moreno said Carcamo has been transferred to a women's prison in Damascus after being arrested some 200 kilometers (120 miles) from the Syrian capital.
In an interview with Syrian public television posted by Chilean media, Carcamo said she entered Syria with her husband.
"I thought that he had come here only for the religion, nothing more. And later I found out what was happening and wanted to return to my country, but he wouldn't let me," she said.
Her mother, Yolanda Carcamo, told local media her daughter traveled to Spain six years ago, leaving behind six children from three fathers.
Moreno noted that the woman previously had run into serious problems in Tunisia, and had asked for help from the Chilean government.
"At that time, she was given tickets to return to Chile, but in the end she didn't use them. She did not return to Chile," the foreign minister said.
Syria has been gripped by deadly unrest since March 2011.
A very large number of the militants operating inside Syria are reportedly foreign nationals.
According to reports, the Western powers and their regional allies, especially Qatar, Saudi Arabia, and Turkey, are supporting the militants operating inside Syria and are providing them with required military equipment.
HH/HH