The presidency was launched with a joint meeting of the Czech government and the European Commission, headed by Commission President Ursula von der Leyen in the eastern Czech town of Litomysl.
In a tweet following the meeting, Czech Prime Minister Petr Fiala said his government had discussed with the European Commission the current problems that concern the EU and Czech citizens.
"One of the main tasks lying ahead of us is the energy self-sufficiency of the EU. If we act unitedly, we have a chance to solve the current crisis," he said.
Von der Leyen said a lot of work lay ahead for the Czech presidency, including energy security, climate protection, economic recovery and digitalization.
"I'm sure we will make good progress on strengthening our energy security while delivering on our climate goals; combining investment and reforms for a robust economy; and deepening our global partnerships," she tweeted.
The Czech Republic joined the EU in 2004, and assumed its first EU Council Presidency in 2009. This year, it has said that its priorities during its presidency will be the refugee crisis and aid to Ukraine, energy security, defense reinforcement and resilience of the European economy.
During a visit to the Czech Republic on Thursday, European Council President Charles Michel said the Czech presidency comes at a "turning point" for Europe.
"Never has our Union faced such great challenges," he said, adding that an informal EU summit will be held in Prague on Oct. 6-7.