The court, while granting their plea, said the "women are here to stay" and since they "work shoulder to shoulder" with their male counterparts, it would "frown upon any endeavour to restrain the progress of women".
While the Army and Air Force allow permanent commission for women, the Navy has limited women officers only to short service commission of 14 years.
Women naval officers were not eligible for pension as it required 20 years of service.
The order came on the plea of several naval women officers, both retired and serving, from the logistics, education and air traffic control departments of the Navy.
The women naval officers in their pleas in the high court had sought similar rights as their counterparts in the other two wings of the armed forces.
They had also alleged gender discrimination, saying while women officers were only entitled to short service commission, men were entitled to both short service as well as permanent commissions.