This means that passengers will probably not be able to enter these two airports, German news agency (dpa) reported.
The workers are employed by private companies that check passengers, staff and luggage at the entrances to the security area on behalf of the Federal Police.
The strike by Lufthansa ground staff begins on Wednesday evening and is scheduled to continue until Saturday morning at 7:10 am (0610 GMT).
Lufthansa passenger flights are expected to face major disruptions on Thursday and Friday. The airline is expecting massive flight cancellations, especially at its hubs in Frankfurt and Munich.
Around 1,000 flights were to be canceled on Thursday and Friday and around 100,000 passengers were expected to be affected, a company spokesman said on Tuesday in Frankfurt.
The airline wants to keep 10% to 20% of normal flights going despite the industrial action.
There have already been two waves of strikes in the current wage dispute for around 25,000 ground staff, each of which paralyzed passenger traffic for around a day.
Verdi has demanded 12.5% more pay and an inflation compensation bonus for one year. Lufthansa has so far offered 10% higher salaries for 28 months.