Only half of the New Territories village houses believed to have illegal structures have been reported to the Buildings Department, despite a scheme offering leniency to people who declare less-dangerous structures that ended on Monday.
A spokeswoman for the department said it had received 18,000 declaration forms. Priority enforcement action will be taken against those structures that have not been reported.
The final figure of reported structures has leapt from 11,000 in the middle of last month but still falls short of initial estimates.
The Heung Yee Kuk rural authority believes that about 35,000 houses built by indigenous male villagers contain unauthorised structures. Emerging rural leader Junius Ho Kwan-yiu said the number could be as large as 200,000, if village houses built by developers were included.
"The government has promised us the structures can stay if they are proved to be safe in five-yearly checks," kuk vice-chairman and executive councillor Cheung Hok-ming said. "It will be difficult for us to protect those who did not report to the government."
Cheung declined to comment on Ho's decision to lobby villagers against declaring their unauthorised structures.
Ho, a lawyer and chairman of the Tuen Mun rural committee, said the declarations would become a record of villagers' building offences. He urged the government to legalise structures that would improve their living.
But his suggestion was snubbed by the kuk and other professional institutes, including engineers and surveyors.
The department did not say when it would start to issue demolition warnings on illegal structures.