The director of conservation for the Galapagos National Park Service, Danny Rueda, called the raticide the largest ever in South America.
The poisoned bait, developed by Bell Laboratories in the United States, is contained in light blue cubes that attract rats but are repulsive to other inhabitants of the islands. The one-centimeter-square cubes disintegrate in a week or so.
Park official Cristian Sevilla said the poison will be dropped on Pinzon and Plaza Sur through the end of November.
A total of 34 hawks from Pinzon were trapped in order to protect them from eating rodents that consume the poison, Sevilla said. They are to be released in early January.
On Plaza Sur, 40 iguanas were also captured temporarily for their own protection.
Asked whether a large number of decomposing rats would create an environmental problem, Rueda said the poison was specially engineered with a strong anti-coagulant that will make the rats dry up and disintegrate in less than eight days without a stench.
It will help that the average temperature of the islands is 75 degrees Fahrenheit (24 degrees Celsius), he added.
The current $1.8 million phase of the project is financed by the national park and nonprofit conservation groups including Island Conservation.
The Galapagos were declared protected as a UNESCO Natural Heritage site in 1978. In 2007, UNESCO declared them at risk due to harm from invasive species, tourism and immigration.
Associated Press writer Frank Bajak in Lima, Peru, contributed to this report.