Azizulhasni Awang competed in the men's sprint on Thursday wearing gloves that had the word "Save" written across knuckles on one hand and "Gaza" over the other. Awang's fists featuring the message were held up to cameras after the race, which took him into the quarterfinals.
The rider said he was expressing a "humanitarian" message, not making a political protest.
"The actions were investigated and we spoke with the Malaysian team management," Commonwealth Games Federation chief executive Mike Hooper said Friday. "It's inappropriate for any form of protest, etc. in a games venue. We respect everyone's right to protest ... however it is inappropriate.
"He has had a strong reprimand from his team management. He's apologized profusely. He now knows any repetition will see a removal of his accreditation."
During Friday's sprint quarterfinal races, Awang wore plain black gloves as he lost to Sam Webster of New Zealand.
"I feel sorry to the people who misinterpret my message. There's no such thing with political protest," Awang, who will also compete in the keirin, wrote on his Facebook page. "It's from the bottom of my heart to express humanitarian (thoughts). Since when (is) expressing humanitarian considered as political?
"Anyway, I apologize to those who think I'm doing wrong and thanks a lot to everyone who always keep supporting ... me. There's no word that I can express it."
Israeli ground troops and Hamas gunmen continued intense battles on Friday in Gaza where more than 800 Palestinians have been killed during 18 days of fighting. The Israeli death toll is 35, among them 33 soldiers, as the country tries to destroy rocket sites in Gaza and tunnels into Israel. Palestinians want an end to the seven-year Israeli-Egyptian blockade of their territory.