Our correspondent says those political parties which supported the original bill are furious and the Islamic parties are now demanding even more changes.
Under the current law, rape victims face prosecution for adultery, unless they produce four male witnesses.
The government had already revised its original draft to satisfy strong opposition from Islamic parties, and critics accused it of rolling back the reforms to make it even harder for women to take action in rape cases.
The government says that this makes it almost impossible to prosecute in rape cases.
Compromise
Law Minister Mohammad Wasi Zafar said on Monday that under the terms of the bill to be presented before parliament, the offence of rape would remain punishable under Islamic law.
The Hudood Ordinance criminalises all sex outside marriage, so if a rape victim fails to present four male witnesses to the crime she herself could face punishment and prosecuted for adultery.
But if a rape victim does not produce four male witnesses, it would be possible for the authorities to prosecute a rape suspect under the secular penal code.
The government says that makes it almost impossible to prosecute a rape case.
"In the case of both adultery and rape, the judge will decide how to try the case," Mr Zafar said.
It proposed putting the offence of rape in the secular penal code where normal rules of evidence apply.
President Musharraf says that women need to be better protected
But it revised the bill because of strong opposition from Islamic parties.
Lawmakers say that the compromise will still mean that rape cases under both systems will remain punishable by death.
A compromise draft was presented, which said that rape would fall under both Islamic and secular penal codes.
Siraju-ul-Haq, a senior member of the six-party MMA religious alliance, told the BBC last month that the government's efforts to change rape laws showed that they were "following a Western agenda to secularise Pakistan".
Human rights activists say this will create confusion, allowing powerful religious lobbies to manipulate what is seen as a weak judicial system.
"The government must focus on more important issues like education, poverty alleviation, price rises and the interference of the military in government affairs," he said.
Mr ul-Haq said moves to repeal the Sharia laws were against "the spirit of Islam".
But Prime Minister Shaukat Aziz criticised the MMA's response to the bill, calling it "shocking".
He said the proposals were aimed at bringing Pakistani law into line with Islamic injunctions promoting women's rights.
