(Repeats story from late Thursday)
* Anti-corruption court deemed unconstitutional
* Junior ruling factions call for abolition of court
* PM wants to preserve the Special Court
By Peter Laca
BRATISLAVA, May 21 (Reuters) - Slovakia's ruling parties clashed on Thursday over whether to scrap a special court dealing with organised crime and corruption.
Corruption and shady connections between political factions and business are common in central and eastern Europe, a region that is still building independent institutions two decades after the fall of communist rule.
A junior Slovak government party, the HZDS, said the Special Court must be abolished following a Constitutional Court ruling which it was illegal for it to pay its judges extraordinary salaries and to demand background checks.
"The (HZDS) considers the Special Court to be a non-standand and ineffective part of the Slovak judiciary," said the party of former Prime Minister Vladimir Meciar, whose government in 1990s was criticised by the West for crony privatisations and crack downs on the opposition.
"Politicians and political parties should respect the verdict ... which stated that creation of the Special Court violates the Constitution," HZDS said in a statement.
The second junior faction, the far-right Slovak National Party, supported scrapping the court.
But Prime Minister Robert Fico defended the institution, which has convicted a mayor for taking bribes and also gangsters who had dissolved victims in barrels of acid.
"It is our duty to respect the verdict of the Constitutional Court, and, if it is possible, to act upon this verdict with legislative amendments so that the Special Court can exist," Fico told a news conference.
When created in 2004, the previous centre-right government said the Special Court had the advantage of being outside regional structures and better protection of its staff by police units, eliminating the chances of external influence.
In the European Union, only Italy, Ireland and Spain have similar specialised courts, said the Slovak Justice Ministry, which has campaigned against the Slovak Special Court.
Global corruption watchdog, Transparency International, has long criticised attacks against the Special Court, and said its abolition would be a step back in the fight against corruption.
"This court has proven that it is not afraid of politicians or the mafia," said Emilia Sicakova-Beblava, the head of Transparency International Slovakia.
"A key factor was that its creation had broken ties between local structures, and their influence over local courts."
Last year, the EU froze millions of euros in aid to Bulgaria because of corruption and crime. In April, the bloc's executive commission started a probe into an a tender worth 120 million euro for services related to handling EU funds in Slovakia. (Additional reporting by Martin Santa; Editing by Angus MacSwan)