The Philippine government plans to move about 100,000 squatters from their homes on crucial waterways in Manila by June as a flood control measure and for their own safety, an official said Saturday.

The plan is to clear six major waterways in the sprawling capital before typhoon season starts in June, while also saving the squatters from being washed away by floods, said Interior Undersecretary Francisco Fernandez.

Experts have long warned that flooding in Manila has been worsened by the squatter communities who build precarious shanties on the banks of waterways, preventing water from flowing freely and blocking drains with rubbish.

Fernandez said there were an estimated 105,000 squatter families living on the waterways of the capital. The 20,000 families -- representing about 100,000 people -- living in the six major waterways would be the first to be moved.

"Forced evacuations will only be taken as a last resort," said Fernandez, whose office is in charge of informal settlers.

He said the government was already meeting those affected so they could be relocated to areas near their old homes or at least in or near the capital.

In the past, he said, squatters relocated outside the capital swiftly returned to their old homes because they could not find jobs at the relocation site.

The government has already allocated 10 billion pesos ($246 million) for the project this year and is preparing "medium-rise buildings" as new homes for the squatters, Francisco told AFP.

Urban planners have said the clogging of waterways by squatters is one cause of frequent flooding and deaths in the capital caused by storms like Typhoon Ketsana in 2009.

In recent months, squatter communities have violently resisted relocation efforts but Francisco said those on the waterways realised they had to move.

"They are there in the waterways not because they want to be, but because they have no other choice," he said.

There are more than 11.8 million people living in the capital and Francisco said as many as 20 percent could be squatters who build shanties in empty lots, under bridges, on waterways or any vacant place they can settle.