Carter's decision brings the military's policy in line with private industry, where a paid three months off is standard after giving birth.
Both policy changes are aimed at retaining women in their late-20s to mid-30s, who leave the Navy twice as often as their male peers.
"Women at peak ages for starting a family leave the military at the highest rates," Carter said in January.
The Air Force and Army had also been considering expanding their policies to 18 weeks.
As far as expanding paternity leave or time off for adoptive parents, the services continue to discuss the idea, which has to be approved by Congress.
"Besides the changes to maternity leave, DoD is working to expand both paternity leave and adoptive leave for service members," the Navy said in a Thursday release.
out NAVADMIN 046/16Reservists may have their active-duty orders extended to cover the leave, as well. The date of pregnancy must be determined by a medical professional.
Women requesting leave should put in for both the maternity leave and additional maternity leave types in the Navy Standard Integration Personnel System, the message said.
While many women lauded the Navy's expansion of maternity leave last year, some pointed out that such a long time away from a command could affect assignment and promotion chances.
The new maternity leave policy addresses this issue specifically.
"No member shall be disadvantaged in her career, including limitations in her assignments (except in the case where she voluntarily agrees to accept an assignment limitation), performance appraisals, or selection for professional military education or training, solely because she has taken maternity leave," according to the message.
Meghann Myers is the Pentagon bureau chief at Military Times. She covers operations, policy, personnel, leadership and other issues affecting service members. Follow on Twitter @Meghann_MT