"Corruption has become endemic within certain classes. This is unacceptable," the church leaders said.
The archbishops also cited rising ethnic tensions in local communities as well as growing concerns throughout the country about the ethnic makeup of government institutions.
Pointing to growing conflicts along the tenuous South Sudan-Sudan border, the archbishops rejected "war as an option to resolve disputes and call upon all parties to implement a meaningful cease-fire and withdrawal of armed forces from the border region."
"We dream of two nations at peace with each other, cooperating to make the best us of their God-given resources, promoting free interaction between citizens, living side by side in solidarity and mutual respect, celebrating their shared history and forgiving any wrongs they may have to done to each other," the message said.
At the same time, the church leaders called upon Sudan to end the "harassment and expulsions" of South Sudanese citizens from Sudan and "for all people to be accorded their human and civil rights regardless of which country they find themselves in."
"We also call for an end to the abduction of South Sudanese by armed groups. We urge our brothers and sisters not to take up arms against fellow citizens but to join the democratization of their countries," the message said.
The archbishops said they were "saddened" by developments in Sudan that has found ethnic, religious and cultural diversity threatened by the government.
In addition, they expressed concern about "growing resentment" against citizens of neighboring countries living in South Sudan. Citing the importance of trade relationships with countries throughout East Africa, the archbishops called for "the cultivation of better relations with our neighbors, guided by the call of Christ to 'love your neighbor as yourself.'"
Saying "the church has not been adequately represented," the archbishops urged the government to broaden involvement in the review of the country's new constitution.
The archbishops pointed to positive developments in South Sudan's first year of existence including road construction, the expansion of telecommunications networks, the issuance of passports, the widening of domestic airline service, the opening of embassies around the world and the development of government institutions.
They also credited the country's officials, working with religious representatives, for addressing ethnic conflict in Jonglei state which led to a disarmament campaign.
"We as a nation -- government, church and citizens -- can be proud of all of this," the message said.