The 13 NGOs demanded in a joint statement that the authorities "abrogate Article 230 and revise all draconian provisions of the Tunisian Penal Code" stating that homosexuality is illegal.
And the justice ministry should order prosecutors to "stop sending detainees for anal examinations as part of police investigative procedures to determine individuals' sexual behaviour," the statement said.
Last week, a court in the central city of Kairouan handed down the maximum term of three years in jail to six students who were found guilty of homosexual activity after being "denounced" by their neighbours.
They were also banned from the city for a further five years.
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Rights group Amnesty International denounced the verdict as "a shocking example of deep-rooted state sanctioned discrimination".
And Human Rights Watch's country director call it "a grave case of infringement on people's private lives and physical integrity".
Amna Guellali described the sentences, which included the "extremely rare" penalty of "banishment", as "mediaeval and not consistent with Tunisia's evolution".
In September, a court sentenced a student to a year behind bars in Sousse on charges of homosexuality, also after he was examined anally.
The youth was released in November pending an appeal hearing expected on Thursday.
After the September judgment, then justice minister Salah Ben Aissa made a controversial call for Article 230 to be scrapped and was sacked in the following month.