However, El-Tom and his assistant, Omer al-Qarray, faced controversy over the inclusion of Michelangelo's famous painting, The Creation of Adam, in Sudanese school textbooks.
The decision was met with strong opposition from some conservative Muslim groups, who argued that the image of God reaching out to Adam in the painting was inconsistent with Islamic beliefs and should not be included in textbooks.
[19] In March 1978, El-Tom chaired and organised the International Conference on Developing Mathematics in Third World Countries, in Khartoum, and The Status and Future of Higher Education in Sudan, in Cairo, in 1998.
[27][33] El-Tom proposed offering financial support to students pursuing education degrees as a means to boost the college's enrollment figures and guarantee the production of well-prepared teachers upon graduation.
[37] In March 2020, following the declaration of the COVID-19 pandemic, the Sudanese Ministry of Education delayed the secondary school exams initially set for 12 April.
[39] In September 2020, the Ministry of Education declared a delay in the school opening date, initially set for the 27th of that month, to 22 November.
Regarding the curricula and their changes, El-Tom believed that the general trend, regardless of the subject, is to take into account the student's age and the readiness of their mind to absorb the material.
Specifically, the painting The Creation of Adam by Renaissance artist Michelangelo caused controversy due to claims of it being heretical.
[46] The situation worsened as a video emerged featuring imam Muhammad Al-Amin Ismail, shedding tears during the Friday Khutbah.
The political secretary of the Justice and Equality Movement, Suleiman Sandal, stated in press statements that "a school curriculum will not be taught to our children that contains images that embody God while we are in the government".
The leader of the National Umma Party, Abd al-Rahman al-Ghali, incited the government to dismiss al-Qarai pointing to Al-Qari's intellectual and political background as a member of the Republican Brotherhood, whose founder, Mahmoud Mohammed Taha, was executed in 1985 on charges of apostasy.
He said that the curricula required a national conference to ensure proper construction of them at a high professional level and societal values and advice, far from politics.
However a member of the Central Council of the Sudanese Gathering of the Teachers Committee, Ammar Yusef, believed that there is a campaign against Al-Qari behind which supporters of the former regime stand.
[50][52] Omer al-Qarray blamed the Minister of Religious Affairs and Endowments, Nasr al-Din Mufreh, for his silence even when some clerics called for his death.
The committee ensured that specialists prepared each subject and that the curriculum met high-quality educational goals, professional and national standards, and was teachable.
[60][61] El-Tom considered his exclusion from the ministry due to a failed security check a “disgrace to his reputation”, which caused him "psychological harm".
[63][64] The Teachers Committee - the leading component of the Sudanese Professionals Association - announced its rejection of the partisan quota of the ministry, and supported El-Tom.
[70] Afterwards, Hamdok demanded that each book of the textbooks be carefully reviewed by authors, language specialists and designers, including illustrators and makers of pictures.
[3] In response to an invitation from the Global Science Program at Uppsala University, El-Tom participated in attending the 2013 Nobel Prize event in Stockholm.