The Australian Greens say the federal government should scrap funding for its chaplaincy program in schools.

Greens senator Sarah Hanson-Young said reports of religious groups possibly breaking federal laws on school religious education by trying to convert students was worrying.

Fairfax Media reported comments from the boss of Access Ministries who said the religious group needed to "make disciples" of students.

"It is quite concerning that we are seeing these type of reports coming out, especially only days after the federal government has announced an expansion of this program," Ms Hanson-Young said in Canberra on Friday.

In the 2011/12 budget, the government increased the national schools chaplaincy program by $222 million.