The CKA claims the design by Future Systems boss Jan Kaplicky broke rules laid down by the International Union of Architects (UIA). It says that the jury should have rejected draft designs which did not meet all the criteria of the contest.
One of the issues is believed to be that in Kaplicky's design books would be stored below ground level - a worrying idea in a city that periodically suffers devastating floods.
But the UIA has hit back, insisting that competition rules were not violated and that there was 'no room for doubt'. A spokeswoman said: 'We had an observer during the interviews and the regulations have been observed.'
CKA has the right to file objections within two weeks of the competition results - announced last week - but does not have the authority to overturn the jury's decision.
Ironically, CKA stresses that it likes Kaplicky's design, which was selected out of 740 international entries. Inspired by sea creatures and described as a 'whimsical, undulating structure', the nine-storey building is a broad pyramid with rounded edges. It will be covered in thousands of champagne-yellow-coloured tiles and is expected to open its doors in 2011.
The scheme will give Kaplicky the chance to build his first major project in his native country.
UK-based Carmody Groarke - the up-and-coming ex-Chipperfield duo - came a close second in the contest, which was judged by a panel including Eva Jiricna, Zaha Hadid and Dominique Perrault.