Construction work on land adjacent to the Lamu sand dunes, the only source of water for the historic town, is in progress and bulldozers have cleared the ground for the project, which belongs to a local politician.
The National Museums wrote to the council clerk that illegal development was taking place in the Shella end of the dunes.
Senior curator Mbarak Abdulqadir, who is also the manager of the Lamu museums and the world heritage site, wrote: "A developer is cutting and flattening the dunes, contrary to the sand dunes conservation plan."
Mr Abdulqadir said the Shella-Kipungani sand dunes are Lamu's only source of reliable fresh water.
A scientific survey of the dunes carried out last year, demonstrated the way in which they absorb and retain water is delicate and earthworks of the magnitude going on could ruin the dunes' ability to preserve water.
Act as a membrane
"The dunes' ability to act as a membrane that prevents the intrusion of saline water from the adjacent coastline into its underground aquifer shall be affected, at the residents' detriment.
We are therefore requesting your office to stop this illegal development," the curator said. "We also wish to inform you that the developer had previously been barred by Nema."
Council clerk Patrick Ouya has written to the developer, area MP Fahim Twaha, to stop construction, saying: "According to the full council minutes of a meeting held on April 8, 2010, it was resolved that the development be stopped until endorsed by the committee," Mr Ouya said.
But Mr Twaha showed the Nation copies of the environmental impact assessment report issued by the National Environment Authority (Nema), authorising the construction and survey records stating that the land on which he is building a six-bedroom house is not within the water catchment area.
Mr Twaha accused foreign property and business owners on Shella Island of fearing competition. The investors, Mr Twaha said, were lobbying for the gazettement of huge chunks of land on the Lamu archipelago by alleging that they were water catchment areas.
He added that the move would serve to create an artificial shortage of land and by pretending to care for the environment, the value of the investors' own holdings would rise at the expense of the local community.
"If this neo-colonial mischief succeeds, the local community would not be allowed to use their own natural resources," he said.
"The sea water cannot climb up to where the wells are to contaminate them, as is claimed" he said, adding: "Water conservation is not the museum's business nor competency. There are no relics, excavation sites and ruins on those dunes."
Among the factors considered in approving Lamu Island as world heritage site is a reliable and sustainable water supply. The source for Lamu is 30 shallow wells formed by dunes that stretch 11km along the island's southern border.
Environment catastrophe
Lamu faces a major environmental catastrophe if its water catchment is not protected.
Besides, conservationists concerned about the archipelago's future, arguing that it could be headed for a humanitarian disaster.
Relevant Links
At the height of the controversy, the district liaison committee gave the Museums the go-ahead to conduct the survey, whose findings were recently presented at the local interested parties' conference.
It is the same issue that was at the centre of the election debacle in the election for the chairman of the council, which saw Cllr Hassan Albeity removed for campaigning against development at the sand dunes.