The board said in a statement that more birds were likely to be found elsewhere in the country.
A police patrol, together with an ornithologist and representatives from the local authority, inspected the Stumholmen area of central Karlskrona on Wednesday morning, said Alexander Vujovic, duty commander at Blekinge police.
The island of Stumholmen is a mainly residential area, and contains a nursery school and the Maritime Museum. No parts of the town have been sealed off yet, Vujovic told TT.
Police say they are waiting for information from the Swedish Board of Agriculture before taking further measures.
Karlskrona town council called a staff meeting on Wednesday morning to discuss the discovery of the bird. The town’s information manager, Joakim Johansson, said he had only limited information.
A press conference will be held at the Maritime Museum at 1pm on Wednesday. The Blekinge county administrative board and the Swedish Board of Agriculture were on Wednesday morning discussing the issues in a telephone conference.’
Before the discoveries in Karlskrona and Oxelösund, six birds had been found with the aggressive H5 virus in Sweden. All had been found in the Oskarshamn area, about 80 kilometres north of Karlskrona. Two of these birds are suspected to have been carrying the H5N1 virus, but confirmation is awaited from the EU reference laboratory in the UK later in the week.
Until the discovery of the greater scaup in Karlskrona, all affected birds in Sweden had been tufted ducks.
H5N1 first arrived in Europe in October, when it was diagnosed in birds in Turkey and Romania. Four children died in Turkey in January after contracting the virus. According to the World Health Organisation, 94 people have died of the virus so far, the majority in Asia.