Vu Kien Cuong, its head, said at a quarterly press meet on Monday that 75 tons of trash and over 2,000 square meters of foam have been collected from the bay since the start of this year.
"Floating garbage gets entangled with rocks and mangrove trees, making collection very difficult."
When the tide rises, this trash flows into the bay, floating everywhere and leaving a bad impression on foreign tourists.
Many tourists visiting have expressed disappointment and outrage that the UNESCO heritage site is being overrun by trash and styrofoam waste, and some have even written to UNESCO about pollution in the Ha Long Bay - Cat Ba archipelago.
Cuong said there are four sources of trash including from dismantling rafts used for farming seafood.
"Trash does not come from tourists."
The water in the bay is also polluted because some old residential areas on shore do not have treatment systems and discharge waste directly into the sea.
Some outdated fishing facilities operating in the bay also discharge waste, he said.
"Quang Ninh Province has never been lax about protecting the environment. When there is garbage, there are campaigns to collect and treat it promptly."
On March 25 authorities launched a month-long cleanup campaign in the bay.
All cruise ships operating in the bay are required to install wastewater and oil treatment systems.
New vessels must have a domestic wastewater treatment system that meets national standards.
Fodor's Travel magazine recently included Ha Long Bay in its annual list of destinations tourists should re-consider traveling to due to its trash problem.