Due to his activism, he has been arrested numerous times by Iranian police. On August 22, 2009, he was arrested again in the context of the unrest after 2009 presidential election. In early March 2010 he was released on bail after spending about three months in solitary confinement. He was charged with Moharebeh for alleged "contact with unspecified foreign groups and working to undermine the Islamic system"  and “insulting the founder of the Islamic Republic Ayatollah Khomeini and Ayatollah Khamenei.” Maleki was hospitalised several times for a heart attack and other physical problems including prostate cancer during his detention. He was also reportedly denied access to an adequate treatment, and later (September 2011), wrote a brief report to the United Nations Special Rapporteur on Iran on the tortures he had suffered during his prison terms for which he was subsequently interrogated and received a notice banning him from travelling abroad.
Maleki at first refused to attend at the Islamic Revolutionary Court, and at the second hearing July 30, 2011 refused to defend himself and said he would not appeal the sentence, because he considered the court of first instance to be illegal. He was finally sentenced on the charge of “propaganda against the system.” He was released but as of 25 January 2012 was summoned to serve a one-year prison term.
In 2013 Maleki publicly apologized for his part in turning away students from Iranian universities leaving them the only option of the Bahá'í Institute for Higher Education, a home based university-class system. The meeting was filmed by film director Mohammad Nourizad and Maleki posted the event to his Facebook page.
- دکتر محمد ملکی بازداشت شد
- Former Tehran University Chancellor Charged With 'Waging A War Against God' RFERL, 7 March 2010
- Iran calls political opponents enemies of Islam By BRIAN MURPHY (AP) 9 March 2010
- URGENT APPEAL: Dr. Mohammad Maleki Summoned to Serve Prison Sentence persian2english.com| January 25, 2012
- compiled/translated by Sen McGlinn from Persian sources (September 25, 2013). "Former Rector of Tehran University apologizes". Retrieved Sep 25, 2013.
- "Former Rector of Tehran University apologises". Facebook account. Mohammad Maleki. Sep 23, 2013. Retrieved Sep 25, 2013.