Local authorities should provide guidelines to businesses on suitable strategies to prevent Covid-19 while remaining open, it said.
The ministry has admitted the model worked in the northern provinces of Bac Giang and Bac Ninh but has not been very effective in the south.
Companies that kept their workers on-site for the last few weeks have said increased stipends for workers and setting up accommodation sent costs skyrocketing, while employees have complained about homesickness and asked to go home.
The ministry requires companies with stay-at-work to test 20 percent of its employees if no Covid cases have been found, and 50 percent if they have.
There are around 600 companies that are currently applying the stay-at-work model in Ho Chi Minh City, where 137,000 Covid-19 cases have been confirmed since April 27.