"It has been brought to my attention that many students are not happy with this decision. I have therefore asked that uniforms be made voluntary rather than compulsory," Ms Raje said on Twitter.
"We are here to provide our girls with whatever they require to excel in their education," she added.
The Rajasthan government had till now maintained that the dress code was being implemented on students' demand saying it had received several complaints on outsiders entering college premises.
"There should be clarity on the identity of students. We have left it on the colleges to decide on the dress colour. We have not imposed any particular colour," state Higher Education Minister Kiran Maheshwari had said.
In a letter by the Commissionerate of College Education, school heads had been directed to decide the dress colour with senior faculty members, student union representatives and submit it by March 12.
The dress code was to be applied to all students as long as they were on campus.
Students, teachers and activists have termed the move regressive and a violation of their right to choose what to wear. The Congress, on the other hand, had accused the government of "pursuing RSS agenda" while protesting the move.