A group of people in the town of Panamericano lunged at medical staff after they announced there were no more shots, according to El Universal newspaper in Caracas.
The disturbance comes as the number of H1N1 cases in Venezuela continues to skyrocket. The number of people with swine flu rose from 12 last week to 179 on Thursday, according to Health Minister Eugenia Sader. Two deaths this year have been attributed to swine flu.
About 200 other people in Venezuela are also being tested for the virus.
Sader said at a news conference Thursday that all of those now being treated have "light cases" and that none of them are in intensive care units.
The health minister said the country would continue administering vaccines against the flu, and has urged all children, pregnant women and those over 60 to get vaccinated immediately.
Sader has continually said the country is not dealing with a public health crisis, but that has not alleviated concerns about the growing epidemic.
In the town of Panamericano, Mayor Mery Carmona urged calm after the fracas.
“People are desperate for the vaccine, and we went through the doses quickly,” she said. Carmona added that the National Guard was called in though local police were able to calm the situation.
“Fear and despair led people to get violent in the town,” she said. “They demanded the vaccine against the H1N1 virus, I ask them to be patient as was have more shots to come”
Dozens of people died in Venezuela in 2009, the year the World Health Organization declared a strain of the virus a pandemic. A few months later, it downgraded it to a seasonal flu.
A swine flu outbreak in Ecuador has killed at least eight people this year and sickened dozens of others.
The Associated Press contributed to this report.