"Police have checked out the first ferries and after inspection they have been authorised to start again," Danish police said in a statement.
German police said a ferry docked in Rodby was searched by Danish police and another one at sea was escorted by a coast guard boat.
Ferry operator Scandlines had said on its website earlier that services had been halted because of "a threat", without giving further details.
"We received a threat by telephone and we didn't have any more information than that so we suspended all traffic," Scandlines spokeswoman Anette Ustrup Svendsen told AFP.
"They cried 'bomb alert' over the speakers, then we didn't know anything more," said passenger Jan Gustavsson, according to local daily Sydsvenskan.
A spate of attacks in Britain and France has heightened fears of terrorism across Europe.
All three countries have experienced deadly attacks in recent years, including truck-ramming assaults in Germany and Sweden.