The female co-CEO of Archie Comics is accused of going on a phallic outburst in the office recently ... allegedly pointing at employees and shouting "PENIS, PENIS, PENIS, PENIS." Oh, Archie!

Archie Comics Publications has filed legal papers against co-CEO Nancy Silberkleit -- claiming she has a history of bullying and sexually harassing employees ... and she must be stopped!

According to the lawsuit, filed yesterday in NY, several employees have lodged complaints about Nancy's "offensive" behavior ... including one time in 2009, when she barged into a meeting and "pointed to each [attendee] and said, 'PENIS, PENIS, PENIS, PENIS' and then walked out."

Nancy allegedly pulled the same "penis" stunt again in 2010 -- but this time she also screamed out, "My balls hurt."

Archie Comics claims it hired an outside firm to investigate the allegations -- and the company recommended Archie cut ties with Nancy ASAP.

Now, Archie wants a judge to grant an injunction -- barring Nancy from returning to the office ... and preventing her from representing the company at the upcoming Comic-Con in San Diego.