The strike affected in particular Air Berlin and Lufthansa connections in the northern German city.
A spokesman for the airport said both terminals were already full with passengers waiting to pass the security checks. But delays were unavoidable with only one of the normal 20 queues open.
The labour action is part of rolling strikes that have been hitting German airports since last month. Along with Hamburg, terminals in Düsseldorf and Cologne/Bonn have been targeted before.
Security staff are demanding an hourly wage of €14.50 and better working conditions. The federal association for safety BDSW offered them €12.75 from March and then €13.50 from January 2013 – but this was rejected by trade union Verdi.
The strike in Hamburg will run through 11pm on Wednesday.