Curriculum objectives
One of the challenges madrasahs face is whether madrasah students can effectively contribute to the knowledge-based economy. Professor Mukhlis particularly asserts that the current objectives of including secular subjects has been "mostly for utilitarian ends," and does not fully embody the true reformist objective of acquiring secular knowledge "as intrinsic to man's rational nature," which was evident in the early madrasahs.
Finances
As private institutions, madrasahs historically receive funding mainly from wealthy Muslim philanthropists or Muslim-based organizations. Today, the issue of funding poses one of the most severe, perennial problems plaguing madrasah education since the 1960s, and is often a contributing factor itself to the other challenges faced by madrasahs. The lack of funds naturally hinders madrasahs from procuring the necessary upgrades to resources, facilities, supplies and infrastructure. Whilst teachers at national schools are among the most highly paid civil servants, madrasahs often face difficulties in attracting qualified teachers due to their lack of funds. In addition, most madrasah teachers receive little training in pedagogy, making standards "rather patchy". In the case of one madrasah, more than S$800,000 was required to finance its annual operations, but only 50% of this was met through fees and miscellaneous grants disbursed by MUIS. Valuable, scarce resources had to be diverted to fulfill the other 50% through fund raising efforts.
The long-standing issue of funding has been noted and discussed on numerous occasions, but without being adequately resolved. The launch of the Madrasah Fund in 1994 allowed madrasahs to tackle existing funding problems with contributions from the public, MUIS and Mendaki, and provided a respite to a certain extent. As of 2012, a total of S$5.18 million were directly disbursed to all six madrasahs from the Madrasah Fund. In addition, an endowment fund was set up by MUIS in 2012 to provide further financing for the madrasahs. Wakaf Ilmu, as the fund is called, is composed of contributions from an Islamic general endowment fund administered by the MUIS, corporate donations, and donations and pledges from the public, including students. As of 2014, the Wakaf Ilmu fund has grown to $6.3 million, more than double the initial amount of $3 million when it was first set up. These funding issues have been repeatedly raised to the Government. In August 2011, an email petition was collated on behalf of the parents of Madrasah Irsyad students calling upon the Government to extend annual Edusave scheme to their children. The Edusave scheme was implemented in 1993 to provide yearly monetary contributions to every student for their holistic development, but madrasah students were conspicuously left out. It was only after 20 years from its inception did the Government decide to grant the annual Edusave grant to madrasah students in 2013. Madrasahs students, however, remain ineligible for Edusave awards. The rationale given by Minister of State for Education, Sim Ann, was that these awards only recognise "secular academic and non-academic achievements in the context of Ministry of Education-funded schools", and are thus inappropriate for madrasahs.
On 23 August 2015, Prime Minister Lee Hsien Loong pledged that the Government will work with the MUIS to strengthen the teaching of secular subjects in madrasahs such as mathematics and science. It will also give financial aid to improve the skills of these teachers, and fund awards for students who do well in them. Speaking in Malay, PM Lee said that it is "important for our religious scholars and leaders to have a good grounding in non-religious subjects. It prepares them to guide Singapore's Muslims to live in a modern, technological society." PM Lee assured that while the Government will help with secular subjects, it will leave religious education in the hands of MUIS and the community. It is reported that these enhanced Government support to madrasahs have enjoyed a "positive response" by madrasah students and staff alike. In 2015, Minister Yaacob Ibrahim announced that madrasah students will no longer have to pay national examination fees, similar to that of other students studying in national schools. These fees will be footed by MUIS and the Ministry of Culture, Community and Youth.
Teaching methodology
In addition, most madrasah teachers receive little training in pedagogy, making standards "rather patchy". Since 2008, MUIS has spent more than S$3 million on teacher training programmes organised in partnership with the National Institute of Education (NIE) and Edith Cowan University in Australia, workshops and seminars. a number of teachers to pursue teaching qualifications at the National Institute of Education in Singapore and at Edith Cowan University in Australia. In November 2007, MUIS and the National Institute of Education jointly launched a specialist diploma course aimed at equipping madrasah teachers with critical pedagogical skills. It is estimated that 90% of the teachers at madrasahs would have sat for the diploma by the end of 2010. By 2012, 73 madrasah teachers have obtained their Diploma in Education qualification and another 76 teachers have graduated from the Specialist Diploma Programme at the NIE. Informally, some teachers have, at their own initiative, tapped into their networks of friends and acquaintances in mainstream schools to arrange for brief attachments to these schools for lesson observations.
National Integration
Another challenge madrasahs face is whether the madrasah students can integrate into the larger society. In 2004, Madrasah Wak Tanjong (located at Still Road) included in its national day celebrations and open house, four teachers and 40 students from Takada Junior High, a Buddhist school in Nagoya, Japan. These teachers and students were part of an ongoing exchange programme with the madrasah.
Risk of radicalization
The general perception that madrasahs are breeding grounds for Islamic terrorists and suicide bombers is so far removed from the truth behind the main roles and relevance of madrasahs in the Muslim world and beyond.