It marks the first rioting charges pressed during the eight weeks of anti-government protests that have rocked the semi-autonomous Chinese city, and those found guilty face up to 10 years in jail.
The protests started in early June against a now-shelved bill that would have allowed extradition to mainland China. The protests have since evolved into a catch-all movement against the local government and are causing disruptions.
The protesters are now demanding an independent inquiry into police action and resignation of the territory's Chief Executive Carrie Lam and democratic reform.
Forty-three of the 44 people charged with rioting appeared on Wednesday at the Eastern Magistrates' Court, where the judge granted them bail, media reports said.
One person did not present herself at court. The judge has issued an arrest warrant and she will no longer be eligible for bail.
The charges, which follow arrests during violent clashes between police and protesters on Sunday, infuriated activists who have demanded that the government avoid using the term "riot" to refer to demonstrations.
In a statement on Tuesday, the police accused pro-democracy protesters of "peace-breaching acts" and attacking police officers.
"They set up roadblocks by umbrellas, wooden planks, bamboo sticks and railing; removed pavement bricks, demolished roadside fences, damaged street signs and lamp-posts, and attacked police officers with lethal weapons, like bricks and sharpened iron rods," the statement said.
On Sunday, protesters defied police orders and organised a demonstration in Chater Gardens and marched through the city centre. Many protesters were wearing black, the colour of the protest movement, and headed for the Chinese government's Liaison Office in the west of the city.
There, in a largely residential area, the police and the protesters clashed. Riot police fired tear gas and rubber bullets at protesters, who set a cart on fire and pushed it in the direction of officers.
Because police had not permitted the march through the city, the protest became illegal the minute demonstrators left Chater Gardens.
News of the charges prompted protests outside two police stations on Tuesday.
Several hundred people gathered in the streets. The police used pepper spray to disperse them. One officer also appeared carrying a shotgun, which he pointed at protesters. The South China Morning Post reported that the gun had been loaded with bean bag rounds.
( With inputs from IANS )