Chief Minister Andrew Barr, the first openly gay state or territory leader, cited his own struggles at school as he announced a decision to provide $100,000 in funding for the program.

"I can say from personal experience in the ACT education system as a teenager, struggling with my own sexuality at that time, that I would have benefited from the support of organisations like the Safe Schools Coalition," Mr Barr said

"School would have been a better place for me in the 1980s if these sorts of services had been available," he said.

"So I consider this to be a fundamental issue of principle, a fundamental issue of what sort of community and society we are."

The Safe Schools program, which provides awareness and anti-bullying support for LGBTI students, has been strongly criticised by conservative members of the federal Coalition.

The program's ambit has been restricted, weakening the power of school principals and requiring participating students to have parental permission, a barrier to kids that want confidential help.

Mr Barr said the Safe Schools Coalition had advised him it could not continue to operate effectively as a result.

"The very clear message that I want to send to LGBTI youth is that it's OK to be gay, it's OK to be lesbian, it's OK to be transgender or bisexual, it's OK to be queer," Mr Barr said.

"Your community supports you, your schools will support you," he said.

Education Minister Shane Rattenbury said the government would not support a "watered-down, sweep-it-under-the-rug approach" from the Coalition.

He said the $100,000 would help ensure the continuance of the program in the ACT.