A landmark floating school that provided classes to children on a lagoon in Nigeria's biggest city, Lagos, has collapsed during heavy rains, its headteacher said on Thursday.

"The structure collapsed at around 10:00 am (0900 GMT) on Tuesday following a rainstorm," the school's director, Noah Shemede, told AFP.

Shemede and the Amsterdam-based architects NLE said there were no casualties and that the floating school in the Makoko area of the city had been empty since March this year.

The headteacher said 58 students who were using the facility as an annexe had been relocated to the main school nearby because of concerns from parents about the effects of annual rains.

Architect Kunle Adeyemi said the building was a prototype which had been used "intensively" over the last three years and a new building would be constructed to replace it.

"We are glad there were no casualties in what seemed like an abrupt collapse," he said in a statement.

"The prototype had served its purpose in time and we look forward to the reconstruction of the improved version amongst other greater developments of the community," he said in a statement.

Makoko has been dubbed the "Venice of Africa" but comparisons between the slum dwellings on stilts in the water and the historic Italian city end there.

The award-winning school, a three-storey triangular A-frame which floated on 250 empty plastic barrels fixed under a wooden base, was the tallest structure in Makoko and had become a landmark.

It provided 200 square metres (2,370 square feet) of floor space and was also used for social events in the desperately poor and neglected fishing community.

Shemede said the debris from Tuesday's storms was being cleared but complained of a lack of government assistance for people living on the water.

"The project is a private initiative for the Makoko waterfront community. The main school was built in 2007/2008 while the collapsed structure was built as an extension in 2012," he said.

"The entire school has a student population of 259. We want (the state) government to assist our community through the provision of social amenities."

Building collapses are common in Nigeria during the rainy season, which in Lagos normally starts in March or April, often because of shoddy building practices and sub-standard materials.

In March, at least 34 people were killed when a building under construction came down in the upmarket Lagos suburb of Lekki.