The ordinance incorporates some of the recommendations of a government-appointed commission in the aftermath of a fatal gang rape in Delhi that led to demonstrations worldwide.
Finance Minister Palaniappan Chidambaram and Information Minister Manish Tewari said Monday the ordinance was signed during the weekend and is law while a bill works its way through the Parliament, NDTV reported.
The president's signing of the ordinance obligates lawmakers to introduce a bill that will replace the ordinance within a short time frame.
Among other things, the ordinance introduces tougher jail terms for crimes against women, including the death penalty for "extreme" cases of rape.
The ordinance replaced the word "rape" with "sexual assault" and included acid attacks and stalking among chargeable sexual-assault offenses.
The day after the Indian Cabinet passed the ordinance, women's groups criticized the move, NDTV said.
"We are alarmed at the complete lack of transparency shown by the government," several groups said in a joint statement issued before Mukherjee signed the measure.
The women's organizations said the government ignored all recommendations that could have empowered women.
"An ordinance like this, implemented by stealth, serves to weaken our democracy. It betrays the trust of thousands of men and women who marched on the streets of Delhi and other cities demanding an end to impunity for sexual violence," said human rights lawyer Vrinda Grover.
State for Home Minister RPN Singh, tried to assure critics the ordinance was not final and that all recommendations would be considered.
"The government is aware that we need stringent laws to protect women," he said.