The Czech Republic can draw up to 53 billion crowns from the programme.
The Education Ministry is solving the problem, deputy education minister for European affairs Michal Zaoralek said.
The Education Ministry has been criticised for long over the drawing of finances from the EU funds.
According to a preliminary report, the EC audit revealed shortcomings in the control system and in several projects carried out both by regions and the ministry.
Education Minister Josef Dobes (Public Affairs, VV) has asked Prime Minister Petr Necas (Civic Democrats, ODS) for a meeting to debate the possible suspension of EU subsidies.
"It is a serious problem of the Czech Republic. Cooperation with other offices, such as the finance and local development ministries, is necessary to solve it," Zaoralek added.
The Education Ministry now expects the EU subsidies payment to be suspended until the situation is redressed.
Zaoralek said the shortcomings dated back to 2008 and 2009 and that the previous ministry's management was to blame for wrong control mechanisms.
"On the basis of the EC audit's recommendations, measures to increase control mechanisms will be taken immediately," Zaoralek said, adding that the programme would not be halted.
Several Czech programmes for the environment, transport and innovations ended up in a similar situation in the past.
Though the Education Ministry´s programme will be probably suspended over mistakes revealed in an audit, the slow drawing of finances is also a problem.
Former education minister Dana Kuchtova was dismissed in 2007 over shortcomings connected with the EU subsidies drawing.
Under the EU rules, by the end of 2011 each operational programme must certify 15 percent of the means it has available in Brussels in this period. To certify means to verify the programme's expenditures.
The Research and Innovations programme had 1.3 percent certified in early December, and in the case of the Education for Competitiveness it was 5.5 percent.
The Education Ministry draws EU subsidies at the slowest pace out of the Czech institutions.
Five people have so far occupied the post of the head of the ministry's section for EU operational programmes. The last one, Robert Plaga, ended on December 28 after spending only a couple of days in office.
The Czech Republic can draw up to 53 billion crowns from the Education for Competitiveness programme by 2013. Another 59 billion crowns are earmarked for scientific projects in the Research and Development for Innovations programme.
Author: CTKwww.ctk.cz
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