It is unclear if Mr Fischer (L) or Mr Klaus will chair upcoming EU summits
A new interim government has taken office in the Czech Republic.
It will lead the country through the last two months of the EU presidency and to early elections in October.
President Vaclav Klaus said the weeks of uncertainty following the fall of the previous administration of Prime Minister Mirek Topolanek were over.
Mr Topolanek's temporary successor is Jan Fischer, the head of the Czech Statistical Office, who has said he holds no long-term political ambitions.
He is supported by the two largest parties in parliament, the opposition Social Democrats and Mr Topolanek's Civic Democrats, as well as the Greens.
After being sworn in as prime minister, the 58-year-old economist acknowledged his cabinet was the result of a temporary deal but insisted it did "not degrade the fact that we are facing urgent, demanding and important tasks".
"We want to complete the Czech Republic's presidency of the EU, prepare the state budget and ensure a quiet and efficient operation of the country until the time when people decide about a new team in the next elections," he said.
"This cabinet will try hard to create a good impression of this country abroad."
Noting that this was the fifth government he had appointed in six years, President Klaus nevertheless welcomed Mr Fischer's arrival.
"The uncertainty after the fall of the previous government has ended," he said. "Today's economic situation requires above all a functioning, hard-working cabinet - and I believe this is what you will be."
The prime minister and president are yet to decide who will be in charge of some of the events being held under the aegis of the Czech EU presidency before the end of June, including the critical summit on the Lisbon Treaty.
On Wednesday, Mr Klaus, a well-known Eurosceptic, said he had no intention for now of ratifying the treaty even though the Czech Senate had approved it.
He said he would wait for any new legal challenges before signing.