Mick Fletcher, a research manager with the Learning and Skills Development Agency, issued the warning at the annual conference of Dysg, the Wales LSDA, in Cardiff.
In a session on regional ("area") inspections of aspects of post-16 learning, he said: "What's going on now isn't actual inspection. Estyn is going into an area that might bring it into disrepute.
"I'm worried about Estyn moving away from its area of real expertise, which is looking at the quality of learning, and becoming an enforcer of government policy."
His remarks followed a report from Bernard O'Reilly, managing inspector for post-16 work-based learning, on three area inspections carried out by Estyn.
One, looking at IT provision in south-west Wales, criticised "a lack of cohesion in the organisations working together", despite awarding the second highest grade (2) and praising the quality of training.
Mr O'Reilly denied that Estyn acts as an arm of government: "At the end of the day we are inspectors. We do it without bias."
Later, he said in a statement: "The questioners simply asked for clarification. Estyn has high-quality expertise in delivering impartial reports."
Dr Haydn Edwards, principal of Menai college, which is awaiting the result of an Estyn inspection, said there was no single quality assurance system in his area.
"I don't know if Estyn's framework is relevant for area inspection," he said.
He also wondered if inspectors' observation of learning sessions was consistent.
Meanwhile, post-16 education funding body ELWa's executive chairman, Sheila Drury, told the conference: "We know we should be doing more for vocational education but we've been saying that since the 1944 Butler Act. We haven't done it well enough. I don't think the answer will come easily and readily, but we must pursue the quest," she said.
Steve Marshall, the new director of the Assembly government's education, lifelong learning and skills department, recognised tensions between promoting academic and practical pathways.
"How do you encourage more people to take up vocational programmes yet boost higher education?" he said.
And Jane Davidson, education, lifelong learning and skills minister, again criticised standards of training for young people offered by work-based learning providers. An improvement plan prepared by ELWa is due to be discussed by the Assembly next Thursday.