Goldie Clarke, 46, received a letter this month from Human Resources and Skills Development Canada (HRSDC) explaining the key containing the personal information of about 5,000 Canadians was missing.
The data belongs to recipients of pensions, old age security, employment insurance and child-care tax credits.
Clarke is worried about someone obtaining data about her disability pension, which helps cover costs incurred by her nine-year-old son.
She said she is concerned about her son's information being stolen, too.
"If they're giving me a benefit for him, under his name, then obviously his name and everything is connected to my file," said Clarke.
Privacy commissioner investigates data loss
In an email, a spokesperson for Human Resources Minister Diane Finley insisted children's information had not been exposed.
The federal privacy commissioner confirmed her office had opened an investigation into the loss of data after the department reported the missing USB in December.
This incident is separate from the probe into the disappearance of a hard drive containing the information of nearly 600,000 Canadians, which became public last week.
That information was lost in early November when a portable hard drive vanished, affecting people who received Canada Student Loans between 2000 and 2006.
At least four lawsuits have been launched against the federal department in relation to the missing student loans data.