Bynes, 27, allegedly tossed the item Thursday night while police were in her apartment investigating a complaint that she was smoking marijuana in the building lobby, the New York Post said.
Bynes, wearing a disheveled blond wig, was charged with a felony count of tampering with evidence, as well as reckless endangerment and marijuana possession.
She was briefly taken to Roosevelt Hospital for psychiatric observation before she was booked at the Midtown North Precinct house, the newspaper reported.
No injuries were reported in the incident.
A judge released Bynes Friday morning without bail, but told the actress a warrant would be issued for her arrest if she missed her court date in July, TMZ said.
The celebrity news website also said the fading starlet has claimed the item police identified as a bong is really a vase.
Bynes is the former star of TV's "The Amanda Show" and "What I Like About You" and the films "What a Girl Wants" and "Hairspray." Her once-bright career has been eclipsed in recent months by reports of erratic behavior, bizarre online rants and motor vehicle offenses.
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