The protesters complained that the report was hurting their business.
Trans TV allowed five of the protesters into the building to hear their complaints, but told them it stood by the report, which was aired on Dec. 31.
"We said it was true and backed up by our findings in the field," said Trans spokesman Ichwan Murni. "We have a duty to inform our viewers about the facts."
The report, which aired Dec. 31, featured a taped confession of a man admitting using rat meat to make the balls, known here as bakso.
The food scare is the latest in a series that have hurt sales at restaurants and small-scale vendors nationwide. Last week, local media reported that dangerous amounts of formaldehyde were being used to preserve fish, noodles and bean curd.