Uribe is facing a double defeat
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Colombian President Alvaro Uribe is facing a major setback to his plans to overhaul the political system and push through austerity measures.
Mr Uribe called a referendum on Saturday to seek public backing for 15 reforms but it seems most did not get enough support to be validated.
Delays in counting mean the full result is not likely to be known until later in the week.
The president has also suffered a reverse in Sunday's elections for the mayor of Bogota, with the government-backed candidate losing to a left-winger.
Lost opportunity
The low turnout in the referendum is blamed on confusion caused by the questions and fear of violence.
President Uribe's office issued a statement on Sunday asking Colombians to be patient and urging election officials to finish the count as quickly as possible.
But Defence Minister Martha Lucia Ramirez has already acknowledged defeat.
"All Colombians have lost an opportunity to adopt structural reforms," Associated Press quoted her as saying.
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REFERENDUM ISSUES
Freezing public workers' salaries
State pensions
Regional auditing offices
Funding education and healthcare
Destination of oil revenues
Congressional voting
Numbers of congressmen
Role of congress
Government funding of regional projects
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Almost all the ballot papers have been counted but around 2% of ballots, mainly from remote provinces, have still to be scrutinised.
"The final result should be ready by Wednesday or Thursday," a spokeswoman for the electoral office told Reuters.
It appears most of the measures received overwhelming support but to pass each point needed to be voted on by at least 25% of registered voters.
Many people appear to have left some sections of the referendum ballot blank, so rendering the result void.
Death threats
Votes have been counted much more quickly in Bogota, where former Communist Luis Eduardo Garzon has won about 46%, with the centre-right candidate, Juan Lozano, trailing on 40%.
Mr Lozano has now conceded victory to his rival.
"Lucho", as Mr Garzon is known, campaigned on a platform of improving education and providing more help for the poor.
His slogan - "No triumphalism, no arrogance" - was intended to set himself apart from the aggressive style of the president.
The authorities are claiming success in the local polls which passed off without major violence, unlike Saturday when at least 13 people were killed and more than 20 wounded.
But the BBC's Jeremy McDermott in Bogota says the rebels had already done a great deal of damage before voting started.
At least 30 candidates were killed and a dozen kidnapped in the run-up to the election, and more than 160 people withdrew their candidacy citing death threats.