"He flew today from Zurich to Prague, accompanied by three Czech police officers," said the Swiss Justice Ministry in a statement.
Pitr had fled his country in 2007 to avoid a six-year jail term for fraud, abuse of confidence and tax offences.
An international arrest warrant was issued for the 40-year-old entrepreneur, who is one of the Czech Republic's most hunted.
In July 2010, he was arrested in a luxury hotel at the ski resort of St Moritz, and has since been detained pending extradition in Switzerland.
Pitr had appealed against the extradition but lost the case before Switzerland's highest criminal court in September 2011.