"Yes, it was a joke," Roque told a virtual briefing.
The remark was made earlier this week when Duterte complained that the country's vaccination effort was hindered by those who are still hesitant to get the injection.
"I know many people are still hesitant. That's the problem, those people who do not want to get vaccinated ... Let's enter their houses and vaccinate them while asleep. End of story", Duterte said, as quoted by the newspaper the Inquirer.
The president also urged the population to comply with restrictions, including social distancing and a requirement to wear masks.
To date, the country has logged nearly 2.7 million COVID-19 cases and slightly over 40,000 deaths.
More than 27.1 million people of the Philippines' almost 110 million people have received at least the first shot, while more than 23.7 million have been fully vaccinated.