The move follows months of accusations by President Nicolas Maduro that Polar, the country's largest private employer, is working to sabotage the economy. The company denies this.
Maduro's predecessor Hugo Chavez expropriated several warehouses from Polar, in some cases arguing that the space should be used to build houses for the poor.
Around 50 workers protested inside the complex, including atop a water tower, with contractors joining them in solidarity outside in a poor neighborhood in the west of Caracas.
"If we don't work, we don't eat," said truck driver Carlos Munoz, a 43-year-old contractor for Polar. He transports food and drink from the site to shops and distributors.
"There's no food in Venezuela and now they do this! How are people going to eat?"
Workers said dozens of national guard and police took over the building on Wednesday evening. National Guard troops remained within the complex. Graffiti on its walls read, "No to expropriation."
Polar said the move puts 2,000 employees' jobs at risk.
"This is our principal dispatch center," company director Manuel Larrazabal said in a statement, adding that Polar sent 12,000 tons of food and six million liters of drink out every month from the site. "We ask that the measure be reconsidered."
The government did not respond to a request for comment.
Nestle spokesman Andres Alegrett said the company was informed by the facility's owner that the area was being expropriated and that the firm was preparing alternative means of distribution.
Other companies renting space at the site include Cargill, Coca Cola, industrial gases supplier Praxair and the clothing firm Zara, according to a statement from Inmobiliaria Carapay, the owner of the complex.
The OPEC nation is suffering what is believed to be triple-digit inflation and shortages of basic goods from shampoo to chicken. Critics blame a failed state-led economic model while the government says an "economic war" is behind the problems.
Polar has said its operations are limited by its inability to obtain dollars to import raw materials.
Authorities told Polar the area was to be used for housing, said a company source who is unauthorized to speak publicly about the issue.
Around 50 people on Thursday rallied outside the complex in support of the measure, chanting, "We want homes."
"Many of us here don't have homes. Chavez promised us homes," said Lindomar Nieves, a 37-year-old mechanic holding a Venezuelan flag.