Outgoing Labor Senator Louise Pratt has used one of her final parliamentary speeches to call for the abolition of the school chaplaincy program, saying it is harming vulnerable gay and lesbian children.

Senator Pratt said a survey found anti-gay chaplains had driven schoolchildren to self-harm and had told them to “pray the gay away”, claims rejected by chaplaincy groups.

The High Court will on Thursday rule whether the $245 million chaplaincy program, and a raft of other government programs, is constitutionally valid.

In a speech to the Senate on Tuesday night, Senator Pratt, who lost her seat at the April Western Australian Senate re-run, said: “I know some great chaplains - they work with love and authenticity, doing wonderful things for our young people. But on a national level we must face the fact that our chaplaincy program is failing Australian young people.”