A City representative said the English club had brought the matter to the attention of UEFA officials, while witnesses gave accounts of "monkey chanting" towards the Italian during his side's 2-1 win in Thursday's round of 32 first leg in Portugal.
The Portuguese champions and Europa League holders were stunned by the accusations.
"What we can basically say is that nothing abnormal happened, no one noticed anything strange, not even the UEFA delegates that worked closely with Porto during the match," Porto spokesman Rui Cerqueira said by telephone.
He went on to describe two chants from Porto and City fans in support of their respective players Hulk and Sergio 'Kun' Aguero that could have been mistaken for other sounds.
"Kun, Kun, Kun; Hulk, Hulk, Hulk," he said, demonstrating the chants. "[Those chants] can be easily confused with racist chants."
He also said Porto had no record of previous racism.
"We are very proud of having a multi-racial team, with players from all backgrounds and to have achieved many titles with respect," he said.
"Porto players have never felt the slightest hint of racism and we were very surprised with the accusations."
However, Manchester City's Ivorian midfielder Yaya Toure said he had "heard something."
"That's why we like the Premier League because it never happens there... maybe in a different country they don't expect black players," he told Sky Sports News.
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Porto fans at the match said abusive chants could be heard.
"Monkey chants were clearly heard, even if for just a brief moment and not coming from the whole stadium, particularly after a nastier foul by Balotelli," supporter Francisco Pimento told Reuters.
"But it all died off afterwards, though Balotelli kept being whistled and booed from then on."
City manager Roberto Mancini said he had not heard anything during the match.
"I didn't hear this because I was concentrating on the game," local media quoted the Italian as saying.
"But I think the players are strong. Mario did very well. He was calm and it is important he contributed.
"He knows these kinds of things can happen every game. This is the reason I spoke to Mario before the game and said: 'you should think only about football'."
Racism is a hot topic in English football at present with Liverpool's Luis Suarez having served an eight-match ban for racially abusing Manchester United's Patrice Evra and Chelsea captain John Terry facing criminal charges over alleged comments he made to Queens Park Rangers defender Anton Ferdinand.
