The crane was attempting to load the container when it tipped over onto the vessel, crashing into the boat and narrowly avoiding two people onboard.
The workers managed jumped into the water as the barge, carrying 600 gallons of diesel, pitched sideways under the weight of the crane into the water.
The ocean around the Galapagos Islands teem with wildlife, including sea lions and penguins, and support a unique and important ecosystem.
Following the incident on Sunday in San Cristóbal Island, the eastern most island in the Galapagos archipelago, park rangers were seen clearing up debris in the waters in an attempt to mitigate the damage.
The provincial Emergency Operation Committee (COE) said they have taken control of the situation.
Norman Wray, Galapagos Minister said: "We have acted in an immediate way. The Galapagos National Park immediately was activated, as well as the national navy, in containment work of the diesel stain."
Staff from the Galapagos National Park and the Ecuadorian Navy used containment barriers, as well as hydrocarbon-absorbing cloth around the vessel to prevent the scattering of any diesel that could leak out from the barge.
Authorities said they have inspected the banks to assess the conditions of the area and measure the possible direct impacts on the ecosystem.