Sanral said it had 1.2 million registered e-tag users and collection of fines was going well.
The agency collected R250.8m in February.
It said it was true that only nine percent of non-registered users paid after Sanral’s seven-day grace period had expired, however 35 percent paid before the seven days were up.
“There is no cash-flow problem but possibly a misunderstanding,” financial officer Inge Mulder said in a statement.
“In fact, we are satisfied with both registrations and payments made by non-registered users. We have always trusted that the public will do the right thing and pay. This high level of compliance has also meant that we are on track to meet our debt obligations.”
The agency was responding to a news report that it could be facing cash-flow problems after recovering less than a 10th of more than R500m in overdue e-toll charges from motorists.
Experts reportedly warned the parastatal might not be able to service its R40 billion debt and might have to ask the Treasury for a bailout.
Sanral denied that it was laying off staff.
“A sub-contractor to ETC [Electronic Toll Collection] is laying off temporary staff because the work they were contracted to do has been completed,” the agency said.