A spokesman for Controller Alan Butkovitz says officials are trying to confirm if the city received the money from title companies, but can't say if it's missing or not.
The city was due a total of about $881.2 million in real estate transfer taxes over the past five years. About 60 percent of that is currently collected electronically.
As recently as 2005, the city received less than 1 percent of its real estate transfer taxes electronically.
A spokesman for Mayor Michael Nutter says the city is working to resolve the issue and improve the record-keeping system.