Speaking to the Jeune Afrique weekly, General Gilbert Diendere said the coup was launched by the presidential guard because of the "serious pre-election security situation" as the west African nation prepares for its first polls since longtime leader Blaise Compaore was overthrown last year.
Diendere, Compaore's former chief-of-staff, said that acting president Michel Kafando and his prime minister Isaac Zida had been put under house arrest.
"They are doing well and will be released," he said.
A transitional government had been charged with running the nation until presidential and legislative elections on October 11.
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Compaore supporters had been banned from running under a controversial law passed in April that made anyone backing "unconstitutional change" ineligible to run.
Diendere said he had taken action as a result of "the exclusion measures taken by transitional authorities" and to "prevent the destabilisation of the country."
He said elections would be held later, without saying when.