The problem was brought into stark focus on Wednesday when several additional trains usually used during the city's rush hour were cancelled because there was no-one to drive them.
But it is not only Munich's public transport that is missing drivers – rail services across the country are facing a similar shortage.
According to a report in the Süddeutsche Zeitung, the problem is due to poor long-term personnel planning.
In the 1990s, many Bavarian train-drivers came from northern or eastern Germany, where widespread unemployment was taking its toll.
But the economic recovery in recent years caused a surge in freight transport and a resulting need for drivers, and many are taking the opportunity to move back north.
One rail spokesman told the paper that the last few months had seen a particularly big wave of departures, and Munich had an extra problem because of the city's high cost of living.
But some put the blame on the rail operators. "The whole sector fell asleep," said Andreas Frank, spokesman for passenger lobby group Pro Bahn. "This has been developing for some time."
Frank believes train-drivers currently have the luxury of choosing where they want to work, and freight offers both better pay and better conditions than public transport.
Munich's public transport personnel also faces other problems – more and more of them are calling in sick, sometimes for psychological reasons. As many as 37 people committed suicide on the city's rail network in the past year, and the drivers affected were often so traumatized that they could not work for months.
Transport operators are now trying to combat their personnel problems by its expanding the three-and-a-half-year training programme to include more trainees.