"Unfortunately we can confirm that two German nationals were killed in Nigeria last weekend," a foreign ministry spokesman told AFP.
"The German embassy in Abuja is seeking clarification and is in close contact with Nigerian authorities."
The ministry did not release further details, either on the victims or the suspected killers.
Regional German newspaper Ostseezeitung said the men, one aged 34 and the other in his mid-50s, were engineers working for German construction company Julius Berger.
Originally from the eastern German state of Mecklenburg-Western Pomerania, they had lived in Nigeria for years and were on a private trip when they were killed last Saturday, the newspaper said.