The claims stem from Dunham's frank new memoir, Not That Kind of Girl. It contains highly personal descriptions of the girls' interactions, including "Grace was sitting up, babbling and smiling, and I leaned down between her legs and carefully spread open her vagina. She didn't resist and when I saw what was inside I shrieked."
Passages like these sparked outrage among conservative members of the American media who accused Dunham of "very disturbing behaviour."
The younger Dunham appeared to be defending her sister in a series of messages on Twitter on Monday night.
"As a queer person: I'm committed to people narrating their own experiences, determining for themselves what has and has not been harmful," she wrote.
She also appealed for the public to "think about how we police the sexualities of young women, queer, and trans people."
Lena Dunham has adamantly denied any impropriety, calling the allegations "upsetting and disgusting."
The outspoken author, who has made a career of telling young women's stories, has since cancelled a number of public appearances in light of the backlash.