The system has been down since Monday evening when the Center of Registers' server room was flooded after a rainstorm.
Paper prescriptions will be made available to patients until E. sveikata (e-Health), the electronic health services system, is brought back online.
"A burst pipe flooded the Center of Registers' server room. The data are safe. All connections have been restored or are being restored," the minister said.
"The worst situation is with E. sveikata. Apparently, those connections will be restored within 24 hours," he added.
Deputy Health Minister Kristina Garuoliene said that the ministry had issued recommendations on how health care establishments should organize their work.
The main task now is to ensure that medicines are available to those who need them, Garuoliene said.
"Our legislation allows using paper prescriptions in exceptional circumstances," she noted.
Saulius Urbanavicius, the head of the Center of Registers, said specialists were working to bring E. sveikata back online as swiftly as possible.