ACL's Managing Director Lyle Shelton said he welcomed news this week that the federal government will provide funding to the state and territory government to administer the program.
However, Mr Shelton said the ACT government is being unreasonable in demanding the program have secular counsellors.
In denying local schools the choice to continue with a chaplaincy program, 27 chaplains will be out of work and hundreds of thousands of dollars of Commonwealth funding will be lost to the ACT.
"When High School Chaplaincy program was introduced in 2006 the purpose and intent was for pastoral care and support," he said.
"The program has been successful and school communities want chaplains in their schools.
"A 2009 national study into the effectiveness of chaplains in government schools found that 98 per cent of principals surveyed believed chaplaincy was making a major contribution to the school's moral.
"Furthermore the same study found that 73 per cent of students surveyed felt their chaplain was highly important in the school," he said.
"It is disappointing the ACT government is denying local schools the choice of extra resources for their school communities because of what appears to be an anti-faith bias."