During a TV address, Nicolas Maduro accused Dia Dia of hoarding food during huge shortages in the country.
This week, soldiers and government workers were sent to branches of Dia Dia supermarket and Farmatodo pharmacy chain to supervise sales.
Venezuela has been in economic crisis after the drop in oil prices.
Analysts say currency controls that restrict the availability of dollars for imports have played a key role in creating the scarcity of many items.
Directors and executives from both Dia Dia and pharmacy chain Farmatodo were arrested on charges of destabilizing the economy.
President Nicolas Maduro did not say that the takeover of the Dia a Dia chain would be permanent.
He said the chain “was waging war against the population” and the national food distribution agency would take over its running.
Nicolas Maduro has said many businessmen are conducting an “economic war”, colluding with the political opposition to oust his government.
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