As the election day neared, security became the most pressing issue for the Commission. The fragile security—including the weak rule of law and human rights violations—was identified by different international organisations such as the UNMIN, the OHCHR-Nepal and Carter Center as the major challenge to a free and fair election. In December 2007, a report on human rights was also published, covering the period since the signing of the Comprehensive agreement by OHCHR-Nepal. The report said that the emergence of armed groups, the escalation of violence among them, and the growing social unrest about issues of exclusion posed a serious challenge for the government and state institutions responsible for maintaining law and order and protecting the rights of the population. The report also raised concerns about the impunity enjoyed by perpetrators of murder and other violence—be they the State, the Maoist cadres or the armed ethnic groups. According to the report, between January and October 2007 around 130 civilians were killed, including 60 people killed by armed groups. These findings indicated that an outbreak of large-scale violence was still the greatest threat to the election.

The already bad security situation worsened two weeks before the election when a bomb exploded in a Mosque in the eastern part of Nepal, killing two Muslims and injuring many others. The international community, and local political party leaders in Nepal started questioning the wisdom of trying to hold an election in such a tense environment.