"This is a problem," Carlos Alvarez, heading up a group of poll observers from South American countries in the Mercosur trade bloc, admitted to La Razon newspaper.
"We hope they find an agreement either before the referendum or immediately afterwards on just one interpretation of the rules," he said.
According to congress, which is relying on the constitution, Morales or the governors can be ousted if the number of 'No' votes exceed the amount of support they received in 2005 elections.
Thus Morales could be forced out if more than 53.74 per cent of voters go against him. The governors can be toppled with just 38 to 48 per cent of ballots.
But the National Electoral Court has offered a very different formula: Morales's bar remains at 53.74 percent, but the proportion needed to bring down a governor is 50 percent plus one ballot.
The uncertainty has heightened pre-poll tensions, which have already sparked isolated incidents of violence.
Morales has found himself unable to travel to many parts of the country that are opposition strongholds.
On Tuesday, Cristina Kirchner, Argentine president, and Hugo Chavez, Venezuelan president, both allies, had to cancel a visit to see Morales in southern Bolivia when anti-government protesters stormed the airport.
If Morales wins the referendum, his political opponents have vowed to not recognise the results.
|Morales's support is strongest among the poor and indigenous [EPA]
"This referendum is illegal. There is no room for a referendum in the constitution. If the president looses he can call for an election but if one of the governors looses he will have to leave right away," Carlos Dabdud, autonomy secretary of the Santa Cruz province, said.
Morales's critic, Manfred Reyes, governor of the central Cochabamba state, has said he would refuse to step down, regardless of the result.
Carlos Tornzu, an analyst, described the political atmosphere in Boliva: "The situation in Bolivia is that 'what I do is legal and what my enemy does is illegal', so right now nobody respects the laws," he said.
The Organisation of American States, which has sent observers, said Bolivia's four million voters needed "security as to how their votes will be counted and how the results will be defined".
But the contradictory rules for the results, and Morales's refusal to negotiate with the opposition, have frustrated voters.
"Most people think the referendum is a distraction from the problems we have, and I don't think it'll change anything really," Pamela Gutirrez, a 25-year-old computer specialist in La Paz, said.Autonomy challenge
Last year, Morales proposed the vote in an effort to undermine the opposition governors who challenged his economic and constitutional reforms - by pushing for autonomy from the central government.
Morales's strongest support is amongst Bolivia's poor and indigenous people.
He has tried to rid the country of inequalities between rich and poor - especially when it comes to the distribution of natural resources during his two and a half years in office.
Half way through a five year term in office, Morales continues to push for social programmes aimed at fighting poverty.
His critics call his approach undemocratic and confrontational and Bolivia's richest provinces have prevented Morales from getting a new draft constitution approved.
Since May, autonomy referendums have been approved in five of Bolivia's nine provinces.