Addressing a gathering of delegates of his right-wing Swiss People's Party, Maurer raised the issue of second-generation Swiss serving in the armed forces, Swiss media reported.
Maurer said that if Switzerland had to intervene in a crisis situation this could be problematic for second-generation Swiss.
In recorded remarks, the defence minister said the civilian population was not as unified as when the country was first formed.
“We have a number of ethnic groups with close relations to their countries of origin that could be influenced by them,” Maurer said, in comments reported by the Tages-Anzeiger.
“What is more around one third of the army is composed of second-generation immigrants.”
The Secondos Plus association that represents second-generation immigrants in Switzerland expressed dismay at Maurer's reported remarks.
“These soldiers are Swiss citizens,” the 20 Minuten online newspaper quoted association co-president Halua Pinto as saying.
“For army members there is no question that they support the country.”
Pinto said the defence minister had to accept that an increasing number of soldiers have a migration background.
“This reflects developments in society,” Pinto was quoted as saying.
Rupan Sivaganesan, a member of the Secondo Plus board, told 20 Minuten the remarks were uncalled for.
“[Xherdan] Shaqiri doesn't score goals against Switzerland,” said Sivaganesan, referring to the Swiss national squad footballer with Albanian-Kosovar roots.
Sivaganesan said the debate was completely unnecessary since Switzerland would never enter into military conflict in Kosovo, Turkey or Sri Lanka.
Army spokesman Walter Frik said the army “made a point of not distinguishing between its soldiers on the basis of country of origin”.
All soldiers had the same rights and duties, Frik told the “Schweiz am Sonntag” newspaper.