Pedro Luis Angarita Azpurua, president of the Farmatodo chain, and his vice president were accused of pricing "irregularities".
They were charged under laws aimed at controlling skyrocketing inflation.
The arrests come days after President Nicolas Maduro ordered the arrests of the owners of the well-known Dia a Dia supermarket chain.
Mr Angarita and his deputy Agustin Antonio Alvarez Costa are accused of understocking shelves and of leaving cash registers unstaffed, thus causing long queues to form outside.
Prosecutors said their actions were intended to lead to speculation and rising prices, which would have a "destabilizing" effect on the economy.
News of the arrest came days after President Maduro ordered the arrest of the owners of the Dia a Dia supermarket chain on similar charges.
President of the Venezuelan Federation of Chambers of Commerce Jorge Roig said the offences the executives had been detained for were "completely subjective".
"We consider it as an attack not only on Farmatodo, but on a specific attack on private industry," he said .
In late January, thousands of Venezuelans attended an opposition march in Caracas, banging empty pots to highlight what they say is the shortage of many staple foods.
Demonstrators also voiced discontent at high inflation, crime and long queues.
Many analysts say currency controls that restrict the availability of dollars for imports play a key role in creating a scarcity of many items.
But President Maduro is adamant that many businessmen are colluding with the political opposition to oust his government.
He has accused four supermarket chains of hoarding goods and smuggling items out of the country.
Venezuela - a major oil producer - has been heavily affected by the fall in oil prices on international markets. The economy officially entered recession in December.
Venezuela has arrested two top executives of one of the country's largest pharmacy chains.