Police officers involved in the arrest of a gunman in Brisbane's CBD yesterday have been praised for their handling of the situation.

The Queen Street Mall was thrown into chaos when a 34-year-old man armed with a handgun threatened to harm himself and others during the busy Friday lunch period in the mall.

The mall was locked down for more than an hour and hundreds of shoppers and city workers were held back behind containment lines as police tried to bring the situation under control.

Fearing innocent bystanders would be killed or hurt, police made their move firing non-lethal pellets into the man's shoulder, legs and hand to end a standoff that brought the CBD to a standstill.

Queensland Police Union president Ian Leavers says it was a terrible situation that could have ended with deadly consequences.

"It was all happening very quickly and police just acted on instinct and they did a tremendous job," he said.

"There were a lot of people around and it could have been a dangerous, dangerous situation.

"Fortunately, no innocent bystander was affected and the public were protected by the police."

Police say the 34-year-old father of three is receiving treatment in the Royal Brisbane Hospital for a gunshot wound to the hand.

No charges have been laid.