El Shaarawy was surprisingly left out of the Milan starting line-up for last weekend's clash with Napoli fuelling rumours of a bust-up with Allegri.
The 20-year-old insists he has no problem with Allegri's team selection and claims he has a good relationship with the manager.
"It was a decision taken by the coach and I fully respect it, like I have always respected substitutions in the past," El Shaarawy told Milan Channel.
"He has given me lots of confidence and shown a lot of belief in me, so there is no problem whatsoever. I respect his choices and, in the game against Napoli, he preferred to start with Robinho.
"There is no problem between the coach and I, we have a good relationship and we always have had. I am relaxed, I have done well until now and I just want to keep improving."
El Shaarawy's agent, Roberto La Florio, also rejected talk of a bust-up and denied talk that the player might be forced to leave the San Siro.
"Allegri is a personality coach and his choice is legitimate, there are no problems," La Florio told RTL.
"Let's not forget that Stephan is a 20-year-old boy playing in one top club like Milan. A future away from Milan? For now I have no reason to even think about it, it is a marriage without crisis."