Cheng Chung-tai upended small China and Hong Kong flags that some pro-Beijing legislators had displayed on their desks in the legislative assembly last October.
The incident happened in a feisty session where two pro- independence lawmakers were barred from taking up their seats in a row over the oath-taking ceremony.
Under Hong Kong law, it is an offence to desecrate national and regional flags by "publicly and wilfully burning, mutilating, scrawling on, defiling or trampling on them".
He said that Hong Kong was facing a "massive purge" against pro-democracy voices.
The city was handed back to China by colonial ruler Britain in 1997 under a "one country, two systems" formula.
But there are concerns China is interfering in the semi- autonomous city, eroding its freedoms and way of life.
Some activists have angered Beijing by calling for greater autonomy or even independence for Hong Kong, with some jailed or awaiting trial over anti-China clashes.
Three other activists had been jailed for three years on riot charges for their role in the same protest.
Other prominent activists were arrested late last month over 2014's Umbrella Movement, which saw tens of thousands occupy the city's streets for 79 days in an unsuccessful campaign for election reform.
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