According to a statement from the Czech government, Fiala discussed with Costa the setting of the European Council's working methods and priorities for the following period, Xinhua news agency reported.
"A number of key decisions await us. The priorities for the new institutional period are primarily the strengthening of security and the increase of competitiveness and economic growth of the EU," Fiala said.
The two leaders talked about the agenda of the next meeting of the European Council that is due to take place in the second half of December. Their discussions also included support for Ukraine, the situation in the Middle East, the future EU budget, and the enlargement of the EU.
Earlier on Thursday, Czech President Petr Pavel also held talks with Costa, during which they discussed "the current challenges and priorities of the Czech Republic and agreed on the need for a united and strong Europe."
Costa, former Prime Minister of Portugal, is set to succeed Charles Michel as head of the European Council on December 1.