The department has proposed so many amendments that members of Parliament say it would be an almost entirely new Bill if the changes were accepted.
But despite the proposed changes, its opponents still reject it and continue to call for its withdrawal.
In an unprecedented move, Minister of Women, Children and People with Disabilities, Lulu Xingwana, said the Traditional Courts Bill is unconstitutional.
She came out strongly on all aspects of the Bill, saying the Bill must be completely overhauled in consultation with rural women.
She pleaded with the National Council of Provinces (NCOP) not to pass the Bill and thereby replace apartheid legislature with this oppressive and discriminatory one.
The slew of changes during the public hearings in Parliament surprised even members of the NCOP's select committee on security and constitutional development – which is processing the Bill – this week.
"This is so different from the Bill that we received and have been dealing with," said ANC MP Amos Gerald Matila. "Are you telling us that you are moving away from your original thinking as the department? This is not what you gave us as the original Bill you introduced to Parliament."
Another ANC MP, Matome Mokgobi, said: "Seemingly, there's likeliness of shifting from the original Bill to this presentation. I'm not sure if I should call this a presentation, a Bill, a new Bill or an amendment. But there is a shift."
This week, presenting submissions to the committee, the justice department sought to address concerns about the effect of the Bill on women living in rural areas, but its proposals did not go down well with non-governmental organisations.
The main suggestion was that traditional courts be integrated into traditional councils, mainly for the purpose of resolving disputes.
Jacob Skosana, chief director for legislative policy in the justice department, said traditional councils are democratic institutions in which all sectors of society are represented. He said the benefits of integration would include sufficient participation by women because they are already involved in traditional councils. But the councils should decide on the quota of women who should participate in traditional councils and their role during sittings.
Currently 33.3% of those who participate in traditional councils are women, according to the department's written submission. It suggested the possibility of increasing the quota to 50%, an option the department of women, children and people with disabilities preferred.
Addressing the call for women to be allowed the option of using a magistrate's court instead of a traditional court, the department suggested the Bill should specifically exclude certain matters from being dealt with formally by traditional courts but allow them to advise, guide, mediate or refer these matters to appropriate people or institutions for resolution.
"The areas in respect of which these exclusions should apply are domestic violence, maintenance, deceased estates, matrimonial matters, issues relating to children in conflict with the law, and land allocation."
In addressing the concept of "opting out" of the traditional justice system, the department proposed that traditional courts be empowered to deal with any dispute, whether criminal or civil in nature, that is not pending or had not commenced in a court of law.
"The councils, and not individuals, will thus be making the decisions. It is suggested that the provisions in the Bill dealing with the designation of traditional leaders as presiding officers be deleted in their entirety," he said.
The Alliance for Rural Democracy an umbrella body encompassing civil society organisations – criticised the department's new proposals, saying they would not fix the fundamental problems with the Bill.
The alliance said the integration of traditional courts into traditional councils would entrench and exacerbate "a fundamental problem identified in most submissions" – the imposition of a separate legal system for people living in the former homelands.
"Subsuming traditional courts into the traditional councils, as created in terms of the Traditional Leadership and Governance Framework Act of 2003, will strengthen Bantustan boundaries. In many areas, disputes about these 'tribal' boundaries, which apartheid imposed, are ongoing, and the councils remain untransformed and undemocratic," it said.