The European Union expressed concern on Tuesday at the state of political and religious freedom in Sri Lanka after a deadly army crackdown on a protest and the vandalising of a mosque.

The EU urged Sri Lanka to ensure speedy investigations into an August 1 incident during which soldiers fired on locals protesting at the contamination of water in their village outside Colombo, killing three people.

A statement also noted the August 10 attack on a mosque by a Buddhist mob which followed a "number of other attacks on mosques and churches" in recent months.

"The right to freedom of peaceful assembly and the right to freedom of worship are fundamental to democratic societies and should be protected by the state," the EU statement said.

Some 50 locals were wounded when the army fired on unarmed civilians protesting at the pollution of ground water supplies, allegedly by a factory discharging chemicals.

Muslim leaders have accused police of failing to stop a Buddhist mob attacking a mosque in a Colombo neighbourhood last Saturday.

The US embassy in Colombo expressed concern at that incident and urged authorities to prosecute those responsible.

The unrest comes ahead of a visit to the island this month by UN human rights chief Navi Pillay, who has demanded an international probe into alleged war crimes by Sri Lankan forces during the final stages of a war against Tamil rebels in 2009.

The European Union has already withdrawn preferential trade concessions after accusing the government of failing to keep its promises to improve its human rights record.

Seventy percent of Sri Lanka's 20 million people are Buddhists, while Muslims make up just under 10 percent.