|Storks are seen in Fuente de Piedra natural reserve in Fuente de Piedra, southern Spain|
The dead great crested grebe was found in the northern province of Alava and a sample sent to the National Reference Laboratory on Thursday revealed "high pathogen" H5N1, the ministry said.
The government has forbidden transport of poultry or bird hunting within a 3 km (1.8 mile) protection zone round the place where the grebe was found and is monitoring within a 10 km radius, the ministry said.
"We have reinforced monitoring of the countryside in order to detect any deaths among wild birds as soon as possible," the ministry said, adding that it would hold a news conference at 4.30 p.m. (1430 GMT)
With cases in Italy and other European countries, experts had said it was only a matter of time before Spain also confirmed it had found an infected bird.
The country has already enforced rules to cover poultry being bred close to many wetlands areas, to prevent contact between migrating birds and domestic fowl.
The Madrid region has ordered all poultry farms to enclose their birds, whether close to wetlands or not, and others may follow suit. But many smallholders in villages also keep chickens unregistered in their backyards.
The European Commission said it had been informed of the test result.
"We have been notified by the Spanish authorities of a confirmed case of highly pathogenic H5N1 bird flu in a wild bird in the Basque Country," said Philip Tod, the Commission's spokesman on health and consumer protection.
"The Spanish authorities are applying the measures required by EU legislation as agreed by member states and the Commission."
"In the protection zone, poultry movements are restricted and poultry must be confined indoors," Tod said.