The 48-year-old singer was seen pointing a fake rifle, with a microphone attached to it, at the audience from a wheelchair causing a huge uproar as it came on the same day where a man opened fire outside a small Baptist church in a town in Texas, killing at least 26 people and injuring 20 others.
San Bernardino was site of one of the deadliest mass shootings in the US history in 2015, where 14 persons were gunned down by two terrorists.
"My art has always been a reaction to popular culture and my way to make people think about the horrible things that happen in this world. My performance was not meant to be disrespectful or show any insensitivity," Manson added.
The singer also said that he had an approval from a police officer to use a microphone during his performance.
"My empathy goes out to anyone who has been affected by the irresponsible and reprehensible misuse of REAL guns," Mansaon said.
The heavy metal and rock singer was injured by a large stage prop at his Hammerstein Ballroom concert in New York on September 30.