The Supreme Court then announced the opposition mayor of San Diego, Enzo Scarano, would be removed from his post and serve 10 months in prison for disobeying a March 12 court order to keep protesters from barricading streets in his city.
The mayors joined opposition leader Leopoldo Lopez, who is being held on charges of arson and conspiracy, as leading government opponents jailed by President Nicolas Maduro's administration since the unrest began last month.
The arrest of San Cristobal mayor Daniel Ceballos was made in Caracas hotel by agents from the Bolivarian National Intelligence Service.
Mr Ceballos, who was in Caracas for a meeting of opposition mayors, had been outspoken in his criticism of what he called repression by security forces in his city.
Interior and justice minister Miguel Rodriguez Torres confirmed the arrest.
He said: "This is an act of justice for a mayor who not only did not meet his obligations as required by law and the constitution, but also facilitated and supported all the irrational violence in San Cristobal."
Anti-government protests have shaken Venezuela for more than a month and a national guardsman was killed in San Cristobal earlier this week.