The one death was unrelated to either abortion or use of the pill, the Food and Drug Administration said. The second woman showed symptoms of infection. One of the women died weeks after her abortion, although it was not immediately clear which of the two.
Four other women have died of a rare but deadly infection after undergoing pill-triggered abortions.
In those four deaths, all involving Californians, the women tested positive for Clostridium sordellii, a common but rarely fatal bacterium.
The FDA has warned doctors to watch for infection by the bacterium. However, the drug, also called Mifeprex or mifepristone, has not been proved to be the cause in any of those cases, the FDA has said.
The recent deaths had sparked renewed calls to ban the abortion pill.
Republican Sens. Jim DeMint of South Carolina and Tom Coburn of Oklahoma urged passage of legislation that would suspend sales of RU-486 after the latest deaths were made public in March. The two want the Government Accountability Office to review how the FDA approved the pill.
The FDA approved RU-486 in 2000 for use in ending a pregnancy up to 49 days after the beginning of the most recent menstrual cycle.
Neither of the two women followed FDA-approved instructions for the pill, which require swallowing three tablets of one drug, followed by two of another drug two days later.
Instead of swallowing the final two tablets, the second course of pills was inserted vaginally in the four women, an "off-label" use that studies have shown effective and that has been recommended by a majority of the nation's abortion clinics. That use does not have federal approval, though studies have indicated it produces fewer side effects.
Last month, Planned Parenthood Federation of America Inc. said it would immediately stop recommending vaginal insertion of the final course of pills. Four of the women who died, including the latest two, received the pills at Planned Parenthood-affiliated clinics. The group said it would work with federal health officials to determine the cause of the infection-related deaths.
Pill manufacturer Danco Laboratories estimates RU-486 has been used 575,000 times in the U.S. since it was approved. It's also been used more than 1.5 million times in Europe.
"We stand behind the safety profile of the drug," Danco spokeswoman Cynthia Summers said.
RU-486 works by blocking a hormone required to sustain a pregnancy. When followed two days later by another medicine, misoprostol, to induce contractions, the pregnancy is terminated.
Federal health officials plan a May 11 workshop in Atlanta to discuss emerging cases of disease involving C. sordellii, which also have included infections in patients who have received skin grafts.
FDA said it has tested batches of the abortion pill but has not found any contamination by the bacteria. Spokeswomen for the agency declined to comment.
The only other U.S. death associated with RU-486 was a case of a ruptured ectopic, or tubal, pregnancy in October 2001. The drug is not to be used by women in those cases.