The parliament passed a "criminal procedure law" last year that experts say contains articles that deny women legal protections.
New York-based Human Rights Watch (HRW) called on Karzai to send the bill back to legislators with amendments.
HRW said the proposed legislation would run counter to a groundbreaking law on Elimination of Violence Against Women passed in 2009, and "follows several other efforts by the Afghan parliament to weaken already inadequate legal protections for women's rights."
Afghanistan's parliament is dominated by conservative clerics and former warlords.
A Karzai spokesman said he could not comment on the president's intentions.