Bachelet endorsed making Chile's coastal waters - more than 5,000-kilometres long and up to 322 kilometres from shore - a whale sanctuary. The proposal still must be approved by Congress.
Chile, which shares economic rights to the waters with Colombia, Peru and Ecuador, has not hunted whales since the 1970s. It was not clear if the other countries would also have to approve the sanctuary.
Bachelet said Chile "wants to give the world a clear sign of its will to protect whales in its waters."
Chilean Foreign Minister Alejandro Foxley opened the five-day conference with a call for the sharply divided commission to find common ground. But pro- and anti-whaling countries immediately clashed.
Great Britain presented numbers it claimed shows that 42 percent of whales killed by Japan were pregnant and a handful were still nursing calves.
Japanese delegate Joji Morishita called the numbers a misinterpretation.
Japan has been at the centre of the commission split as it continues to hunt whales - despite a 22-year commercial moratorium - under a provision that allows whaling for scientific purposes.
Opponents insist its activities are for commercial purposes. Japan insists that the world whale population has grown to a level that makes hunting possible.
The commission's scientific committee described difficulties in counting the world's whale population.
"While there is no easy answer to the question 'How many whales are there?' it is clear that stocks are ... for the most part in a precarious state of conservation," a committee report stated.
Commission members said they will likely table any controversial proposals, including Japan's request to commercially hunt whales in four of its coastal communities and a plan by Latin American nations for a whale sanctuary in the southern Atlantic Ocean.
