According to Maduro, the owners reduced the number of employees working at cash registers so as to deliberately create queues and "annoy the Venezuelan people."
"Yesterday we detected that a famous chain of stores was conspiring, irritating the people. We came, we normalized sales, we summoned the owners, we arrested them and they're prisoners for having provoked the people," Maduro said.
He pointed the finger at Venezuela's business elite, who he claimed are collaborating with the country's political opposition to overthrow his socialist government via an "economic war."
Maduro also blamed four supermarket chains for hoarding goods and smuggling items out of Venezuela.
He said that "those who use their stores to hurt the people will pay with time in prison."
The warning came a week after thousands of people came to the streets in the capital Caracas, banging empty pots in a show of protest against the alleged shortage of many staple foods, long queues, high inflation and crime.
A major oil producer, Venezuela has been hard hit by plummeting oil prices on international markets.
The country's economy has officially been mired in recession since December 2014.