Prime Minister Ivo Sanader told reporters at government headquarters that according to experts and all information available "there is no threat to human health."
He added that samples would be sent to a reference centre in Great Britain on Saturday to see if it was an H5 N1 virus.
Results from the Weybridge laboratory are expected in about two days.
Sanader further said that a team of experts in charge of monitoring avian influenza would be in constant contact with the government.
The crisis management team is headed by Agriculture Minister Petar Cobankovic and Health Minister Neven Ljubicic.
The government has taken all the necessary steps to contain the virus.
The prime minister said that relevant authorities had notified the European Commission, the World Organisation for Animal Health and neighbouring countries of the finding.
"The Croatian government wishes to warn all Central and Southeast European countries about (the virus) and about the need for a constant exchange of information," the prime minister said.
Later on, Agriculture Minister Petar Cobankovic told an emergency press conference that there was no reason for panic.
"There is no substantial risk of the disease being transmitted to humans," Cobankovic said.
According to Cobankovic, a suspicious flock of swans was sighted at the Grudnjak fish farm near Orahovica, about 200 kilometres east of Zagreb, on 19 October. Samples were taken from the swans and sent to the Centre for Poultry Farming at the Veterinary Institute in Zagreb for testing.
"The H5 virus was confirmed at 1700 hours today," the minister said.