Froehlich expressed concern that Edathy may have been warned ahead of the investigations.
Police raids on Edathy's houses in the state of Lower Saxony and in Berlin and his offices near Hannover on Monday and Wednesday produced very little evidence relevant for an investigation.
Investigators found only two computers and parts of some damaged computer hard drives, he said.
The authorities are trying to find out who could have alerted Edathy ahead of the the raids and the prosecutor's office will launch criminal prosecution against those responsible, he said.
The SPD's top leaders, who received the intelligence information from Friedrich, said they have not given any tip-off to Edathy and they kept the information secret. They said Edathy has been on a medical leave since the beginning of January and they have no information about his whereabouts.
Merkel said she accepted Friedrich's resignation with great regret.
She expressed her deep appreciation of Friedrich's contributions, especially his efforts as the interior minister to reorganise the country's security organisations after the neo-Nazi murders came to light and to strengthen the operations of counter-terrorism organisations at the Federal and state levels.
A successor to Friedrich will be found in consultation with Horst Seehofer, chairman of the Christian Social Union (CSU), she told a news conference. Friedrich is a member of the Bavarian CSU, which is a sister party of Ms Merkel's Christian Democratic Union (CDU).
