Although the use of the cluster randomized trial (CRT) design to evaluate vaccines, public health interventions or health systems is increasing, the ethical issues posed by the design are not adequately addressed, especially in low- and middle-income country settings (LMICs). To help reveal ethical challenges, qualitative interviews were conducted with key stakeholders experienced in designing and conducting two selected CRTs in Malawi. The 18 interviewed stakeholders included investigators, clinicians, nurses, data management personnel and community workers who were invited to share their experiences related to implementation of CRTs. Data analysis revealed five major themes with ethical implications: (1) The moral obligation for health care providers to participate in health research and its compensation; (2) Suboptimal care services compromising the integrity of CRT; (3) Ensuring scientific validity and withholding care service; (4) Obtaining valid consent and permission for waiver of consent; and (5) Inadequate risk assessment for trial participation. Understanding key ethical issues posed by CRTs in Malawi could improve ethical review and research oversight of this particular study design.