In the June 5 incident, 10 aircraft disappeared from radar screens while on June 10, a further three went missing.
On each occasion, Austrian authorities brought in more controllers in order to talk with the aircraft and maintain order.
"Planes disappeared from screens for a matter of seconds, here and there. The outages were sporadic and not grave," said a spokesman for German air-traffic control. "It must have been an external source of disruption. We are trying to identify the causes."
Der Kurier, an Austrian newspaper, suggested that a targeted cyber attack may have caused the disappearances. The paper also claimed the aircrafts' transponders may have been interfered with, but that, it stresses, would have required the use of a satellite.
Eurocontrol, a European air-management agency, and the European Aviation Safety Agency have started an investigation into the two incidents.
"Given the potential impact of the incident on safety, capacity and radio frequencies the Eurocontrol Network Manager immediately started an investigation," Eurocontrol said in a statement.
But so far experts are at a loss to explain what caused the aircraft to disappear.
At first a Nato electronic warfare exercise in Hungary was suspected as the cause of interference as it coincided.
The exercise, apparently, used devices designed to interfere with enemy radar and there were suspicions it may have affected civilian flights.
But Hungary's defence ministry denied any Nato involvement, saying the technology used was weak and had a range of only 4,000 metres – a height well below the altitude of the aircraft.
Deepening the mystery is the fact that the second incident occurred after the exercises had finished.