They said tension between the two communities and further acts of revenge by both sides are likely to continue until those responsible for planning these atrocities are brought to justice.
It was alleged that Nigerian police deployed to quell violence between Muslims and Christians in the northern city of Kano used excessive force and may have committed dozens of unlawful killings in the name of restoring law and order.
The Human Right Watch challenged the police to attempt providing security and not kill more people as the situation was volatile.
A source in Kano was quoted saying that the situation was quite bad and it was likely to spill over to other states if community leaders and politicians were not careful. "We are very worried indeed but hope the situation will improve," said the source.
They want police authorities to give strict instructions to the security forces deployed in anti-riot situations in Kano and elsewhere to only use lethal force as a last resort and to use all other possible means to arrest suspected criminals.
Agency for Co-operation and Research in Development, ACORD which runs Area Programmes in Negeria, Chad, Cameroon and Niger is among the civil organizations that have raised concern over the deteriorating situation in the two Nigerian States.
Both houses of Nigeria's parliament have approved the state of emergency in the central state of Plateau declared by President Olusegun Obasanjo.
The president ordered the measure to control continuing violence between the state's Muslims and Christians.
Several opposition politicians have already condemned the move as undemocratic.
President Obasanjo said serious action was needed to deal with a situation that he called "near mutual-genocide".
Earlier, the newly appointed governor of Plateau, Chris Ali, made a call for peace in the troubled state, warning that if Nigerians wanted to see where hatred and intolerance could lead, they should consider what happened in Rwanda.
Hundreds of Muslims were killed by Christian militants in the town of Yelwa earlier this month. In February, 49 Christians were killed in a church.
Meanwhile, Christians have reacted angrily to the president's statement. Speaking for the Christian Association of Nigeria, the head of the Anglican church, the Most Reverend Peter Akinola, demanded a state of emergency also imposed on Kano State in which Christians had recently been killed.
At the National Assembly in the capital Abuja, Senator Tokunbo Afikuyomi of Lagos State, also condemned the decision.
This sentiment was echoed by leading Nigerian human rights lawyer and long-standing critic of President Obasanjo, Femi Falana.
Kano state has a population of 5.6 millions and cover an area of 20,760sq. Km with one emirate Kano.