The crew of the Werra scramble to gear up in life vests and helmets. Guns are at the ready, with the team prepared for any trouble, fingers on triggers.
It proves a false alarm - just a Libyan fishing boat that didn't answer initial radio calls.
Salam Sayed, a German soldier of Egyptian origin, speaks to them in Arabic and all is back in order.
But half an hour later, there's another alert: Argos, one of the boats chartered by medical charity Doctors Without Borders (MSF) to help rescue migrants, has reported another boat adrift 80 kilometres (50 miles) off the Libyan coast.
This time it's a large dinghy loaded with migrants, struggling in the waves.
The German ship immediately sends out two of its boats to the dinghy – one to make contact with the people on board and the other for additional security.
But there is no threat and the two boats, along with one sent by Argos, begin to transport the migrants back to the Werra.
One by one the 96 men, 42 women and two children board the big ship, welcomed by crew dressed in masks and white protective suits.
Crew members then help the migrants from one procedural step to the next, gloved hands on weary shoulders.
Everyone is photographed and gets a plastic bracelet with an identification number. All personal belongings are meticulously searched and then placed in envelopes for retrieval when they leave.
Most of the migrants come from Nigeria, Ghana, Senegal and Sierra Leone. Once on the Werra, they follow orders silently, looking a bit lost.
'It was my dream'
The medical staff tends to some of the weaker migrants. Many receive sheets and pillows so they can rest on a rear deck of the ship, some opting to lie out in the sunshine.
Crew members in their protective plastic suits walk around giving water bottles to people - gesturing in explanation because of the language barrier.
They quickly hand out meals to the exhausted migrants so they can go and sleep.
Several men and women sit in a circle, holding hands in an improvised prayer of thanks.
This is the third rescue operation of this kind for the Werra, which has about 100 crew members and has been involved since July in the European Union's military operations.
"The emotion really changed. The crew members like to help, they enjoy helping, and after the operation there is an enthusiastic feeling," said Christian Lueders, the ship's chaplain.
The European mission to intercept smugglers' boats and rescue migrants has saved thousands of lives since it was initiated in late June.
The operation was initially called EUNAVFOR Med, but on Monday, the EU announced it had been renamed Sophie, after a baby girl who was born on a German rescue ship, the Schleswig-Holstein, that picked up her Somalian parents off Libya on August 22.
The mission comprises four ships, including an Italian aircraft carrier, and four planes. It is manned by 1,318 personnel from 22 European countries.
Lueders said that while some German sailors are worried how the unprecedented migrant influx could change their country, the crew is delighted to be able to save lives.
Sayed, who joined the army last year specifically for these types of missions and whose family in Frankfurt pays subsidised rent as refugees, said these missions make him proud.
"It was my dream to do anything to help these people," he said.
"They put their own lives at risk for their children, just to flee and try to find better chances in another country."