Rijeka youth coach Ranko Buteka also denied any of his players racially insulted any City player during the game, saying City coach Patrick Vieira may have led his team off at halftime because Rijeka were too strong for them.
The game was stopped after an alleged incident of racist abuse against City's 19-year-old French midfielder Seko Fofana just before halftime.
Fofana had been shown a red card for an off-the-ball incident just before the match was abandoned.
Vieira, City's elite development coach, then led his players off after Fofana was allegedly abused by one of the Rijeka team.
Rijeka were leading the match, played in Novigrad, western Croatia, 1-0, when the incident happened.
"After our first goal, we expected more pressure from City but we remained the dominant team in all departments and had several opportunities to score again," Buketa told Croatia's national news agency Hina.
"They responded with more aggression, which resulted in a red card for them.
"While the first tougher tackle on Dangubic could be classified as reckless, the really violent tackle on Marko Marcius only a minute later was unjustifiable, so the Manchester midfielder was rightly sent off.
"What ensued was something rarely seen, even in friendly games.
"The Manchester coach, Patrick Vieira, entered the pitch, discussed something with the referee and then, to the utter surprise of the packed stadium, withdrew his team from the pitch. The reasons are known only to him.
"Perhaps he had expected an easier rival, against whom they could easily dominate and easily score, but this wasn't the case against us."
In a statement carried by Hina, the club rejected any racist allegations.
"We also want to point out that HNK Rijeka, in cooperation with FARE (Football Against Racism in Europe), has been supporting the campaign against racism for years and we strongly condemn every such incident.
"We are very unpleasantly surprised by the serious and unfounded allegations, which we entirely reject."
In an updated statement on their website (www.mcfc.co.uk) City said the match was abandoned for an "alleged incident of racial abuse."
"Details remain sketchy at this stage, but club representatives in Croatia and Manchester are liaising with officials, match organisers and the Croatian FA to pursue this matter fully."
UEFA, European soccer's governing body, has fined the Croatian FA for racism in the past, most notably at Euro 2012 when the country's fans racially abused Italian Mario Balotelli.
Croatian fans were also cited for displaying far-right flags and symbols at the World Cup in Brazil but were not fined by FIFA, world soccer's governing body.
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