Czech President Milos Zeman has called for the Czech Republic to hold a referendum on European Union and NATO membership following Britain's shock vote to leave the EU, a suggestion quickly rebuffed by the government.

Zeman said on Thursday he would back his country staying in the EU and NATO.

He has no power to call a referendum, but is an influential leader in a country where euroscepticism is widespread. The Czech Republic joined the bloc in 2004.

"I disagree with those who are for leaving the European Union," Czech Radio quoted Zeman as saying at a meeting with citizens in the eastern town of Velke Mezirici late on Thursday.

"But I will do everything for them to have a referendum and be able to express themselves. And the same goes for a NATO exit too," the centre-left president said.

Britain's 52 to 48 per cent vote on June 23 in favour of quitting the EU has emboldened eurosceptic groups across Europe and raised concern other member states may consider leaving.

The Czech government responded swiftly to Zeman's suggestion.

"Membership in these organisations is a guarantee of stability and security," Prime Minister Bohuslav Sobotka's spokesman said in a statement.

"The government is not considering taking any steps which would question in any way our membership and the long-term orientation of the Czech Republic's foreign policy. Therefore it does not envisage any referendum."