The launch has already been postponed twice since Friday due to adverse weather conditions.
"Following an anomaly observed during the countdown for the launch of Soyuz flight VS14 carrying Sentinel-1B, the countdown was halted," ESA said in a statement.
The launch vehicle and satellites have been switched into a completely safe standby mode, the EU space agency said. The new launch date will be announced after the anomaly has been analyzed.
Sentinel-1 is the European Radar Observatory that is the first new space component of the Global Monitoring for Environment and Security satellite family developed by ESA and paid for by the European Commission.