Police came to arrest Vladimir Prokop at his office at the National Agriculture Museum, close to the Interior Ministry.
He fled through the exhibition halls of the museum, an emergency exit staircase and then hailed a cab, television Nova reported.
“He was an ordinary, even compliant man, nobody thought he would turn out to be a world-class trickster,” the museum spokesman Lubomir Marsik said.
The money stolen amounts to roughly a third of the annual budget of the museum.
Most of it was found in plastic bags at Prokop’s flat.
Prokop got the job at the museum under a false identity, presenting himself as a trained economist.
Calls to his phone number, still listed on the museum’s website, went unanswered.
He escaped last June from prison where he was serving time for embezzling 10m Czech crowns from the Prague branch of the Evangelical Church of Czech Brethren, where he managed its foreign donations, Czech news agency CTK said.