Sudan's southern former rebels, now government partners, have strongly condemned the decision to expel UN envoy Jan Pronk.
Riek Machar said several aspects of last year's deal had not been implemented
South Sudan Vice-President Riek Machar told the BBC his group had not been consulted over the decision, taken over Mr Pronk's comments on the Darfur war.
"His expulsion is going to make things worse in Darfur, Mr Machar said.
The former rebels joined the government under last year's peace deal but correspondents say relations are sour.
Mr Machar said that Mr Pronk had been appointed in consultations with both sides in the 21-year north-south war and his mission was not only related to Darfur.
BBC Africa analyst Martin Plaut says the incident is the latest rift between the two groups which signed a peace agreement in January 2005 ending decades of civil war.
The comprehensive peace agreement signed between Khartoum and the former rebels of the Sudan People's Liberation Movement (SPLM) was supposed to end tensions between the mainly Muslim north of Sudan and the Christian and animist south.
SPLM leader Salva Kiir is national vice-president and there are several southern ministers in the government.
But our reporter says northerners believe the southerners are interfering in their affairs by supporting the deployment of UN troops in Darfur - something that President Omar al-Bashir is implacably opposed to.
The SPLM argues that Darfur is a national issue, and one in which they should fully participate.
The former rebels are also furious that the difficult question of the status of the oil-rich region of Abyei, which lies between north and south has still not been resolved.
President Bashir has refused to accept the findings of a boundary commission designed to settle the issue, while Chinese and Malaysian companies continue to pump oil from the region.
Mr Machar told the BBC's Focus on Africa programme that there were other parts of the peace deal which had not yet been put into effect:
- The training of a joint military unit
- The civil service commission to divide state jobs between north and south
- The national petroleum commission to share oil revenue
The south now feels marginalised, and anger over the issue is growing, our reporter says.
Some commentators warn that the peace agreement signed with so much fanfare in 2005 is now under serious threat.