"We have refused to approve the final statement because it is different from the protocol agreement which we have signed," said Ibrahim Assaley, the Tuareg rebel National Liberation Front of Azawad, FNLA.
Moussa Ag Asherif, close to Ansar Dine head Iyad Ag Ghaly, confirmed the impasse in talks which came just 48 hours after the two groups announced their plans for joint domination of the remote desert region.
Asherif said the original accord had been merely a basis for working discussions and that the deal was on a "take it or leave it" basis. Ag Ghaly is to travel to Gao where the discussions are taking place on Tuesday morning "to solve the problem”.
A draft of the statement by Ansar Dine spoke of applying "pure and hard" Islamic Sharia law and banning non-Muslim humanitarian groups from the area.
The original declaration of a separate Islamic state in Mali's vast desert north, an area larger than France, had come at the weekend.
In January, the Tuareg rebels launched an offensive against the Malian army, which was heightened with the arrival on the scene of Ansar Dine, which wants Islamic Sharia law imposed throughout the land-locked west African nation.
"The government of Mali categorically rejects the idea of the creation of an Azawad state, even more so of an Islamic state," Hamadoun Toure, information minister in the transitional administration, told the French news agency on Sunday.
The West African bloc Ecowas on Monday also rejected the rebel declaration of independence and repeated an earlier threat to take "all necessary measures" to keep Mali intact.
It said the move would "only worsen the situation for a population that has already been the victim of all sorts of atrocities and hardships in the occupied area of Mali, as well as expose the entire region to the most serious dangers regarding peace and security".