A bill to amend the Islamic laws, including the one that requires rape victims to produce four male witnesses or risk an adultery charge, has been fiercely opposed by the conservatives.
Women's rights activists had welcomed the proposed amendments, that would have put the crime of rape in the penal code, although some said the changes did not go far enough and the Islamic laws should be repealed altogether.
But in the face of the objections from religious parties, the government said on Monday rape would remain in the Islamic law, although it would also become a crime under the penal code.
"If there are four witnesses it will be tried under (Islamic law), if there are not, it will be tried under the penal code," said Law Minister Mohammad Wasi Zafar.
"In the case of both adultery and rape, the judge will decide how to try the case," he told reporters.
Controversy over the laws, known as the Hudood Ordinances, mirrors divisions in Pakistani society where a small class of urban liberals is often at odds with more conservative, religious groups.
The laws, which laid down punishments for such crimes as rape, theft and adultery were introduced in 1979 by military ruler Mohammad Zia-ul-Haq and have drawn widespread criticism both at home and broad.
President Pervez Musharraf, who promotes an ideology of "enlightened moderation", had earlier assured rights activists he would back any moves to amend or repeal the laws.
Zafar said a draft of a new amendment bill would be presented to parliament for debate on Wednesday.
Supporters in parliament of the original amendments said they would wait until seeing the new draft before commenting.
Leader of an opposition alliance of religious parties had threatened to withdraw from the national and provincial parliaments if the original amendments were passed.
The alliance said it objected to any changes that contradicted the Koran.
Musharraf left on Monday for visits to Europe and the United States where he is bound to face questions about human rights, in particular the plight of women, in his overwhelmingly Muslim country.